1
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Zheng J, Lin XJ, Xu H, Sohail M, Chen LA, Zhang X. Enzyme-mediated green synthesis of glycosaminoglycans and catalytic process intensification. Biotechnol Adv 2024; 74:108394. [PMID: 38857660 DOI: 10.1016/j.biotechadv.2024.108394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 05/23/2024] [Accepted: 06/07/2024] [Indexed: 06/12/2024]
Abstract
Glycosaminoglycans (GAGs) are a family of structurally complex heteropolysaccharides that play pivotal roles in biological functions, including the regulation of cell proliferation, enzyme inhibition, and activation of growth factor receptors. Therefore, the synthesis of GAGs is a hot research topic in drug development. The enzymatic synthesis of GAGs has received widespread attention due to their eco-friendly nature, high regioselectivity, and stereoselectivity. The enhancement of the enzymatic synthesis process is the key to its industrial applications. In this review, we overviewed the construction of more efficient in vitro biomimetic synthesis systems of glycosaminoglycans and presented the different strategies to improve enzyme catalysis, including the combination of chemical and enzymatic methods, solid-phase synthesis, and protein engineering to solve the problems of enzyme stability, separation and purification of the product, preparation of structurally defined sugar chains, etc., and discussed the challenges and opportunities in large-scale green synthesis of GAGs.
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Affiliation(s)
- Jie Zheng
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 210023 Nanjing, China
| | - Xiao-Jun Lin
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 210023 Nanjing, China
| | - Han Xu
- Jiangbei New Area biopharmaceutical Public Service Platform, 210031 Nanjing, China
| | - Muhammad Sohail
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 210023 Nanjing, China
| | - Liang-An Chen
- School of Chemistry and Materials Science, Nanjing Normal University, 210023 Nanjing, China
| | - Xing Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 210023 Nanjing, China.
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2
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Ichikawa M, Otsuka Y, Minamisawa T, Manabe N, Yamaguchi Y. NMR characterization of uniformly 13C- and/or 15N-labeled, unsulfated chondroitins with high molecular weights. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2024; 62:439-451. [PMID: 38235950 DOI: 10.1002/mrc.5426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 11/06/2023] [Accepted: 12/21/2023] [Indexed: 01/19/2024]
Abstract
Solution nuclear magnetic resonance (NMR) analysis of polysaccharides can provide valuable information not only on their primary structures but also on their conformation, dynamics, and interactions under physiological conditions. One of the main problems is that non-anomeric 1H signals typically overlap, and this often hinders detailed NMR analysis. Isotope enrichment, such as with 13C and 15N, will add a new dimension to the NMR spectra of polysaccharides, and spectral analysis can be performed with enhanced sensitivity using isolated peaks. For this purpose, here we have prepared uniformly 13C- and/or 15N-labeled chondroitin polysaccharides -4)-β-D-glucuronopyranosyl-(1-3)-2-acetamido-2-deoxy-β-D-galactopyranosyl-(1- with molecular weights in the range from 310 to 460 k by bacterial fermentation. The enrichment ratios for 13C and 15N were 98.9 and 99.8%, respectively, based on the mass spectrometric analysis of the constituent chondroitin disaccharides. 1H and 13C NMR signals were assigned mainly based on HSQC and 13C-detection experiments including INADEQUATE, HETCOR, and HETCOR-TOCSY. The carbonyl carbon signal of the N-acetyl-β-D-galactosamine residue was unambiguously distinguished from the C6 carbon of the β-D-glucuronic acid residue by the observation of 13C peak splitting due to 1JCN coupling in 13C- and 15N-labeled chondroitin. The T2* and T1 were measured and indicate that both rigid and mobile sites are present in the long sequence of chondroitin. The conformation, dynamics, and interactions of chondroitin and its derivatives will be further analyzed based on the results obtained in this study.
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Affiliation(s)
- Megumi Ichikawa
- Central Research Laboratory, Seikagaku Corporation, Tokyo, Japan
| | - Yuya Otsuka
- Central Research Laboratory, Seikagaku Corporation, Tokyo, Japan
| | | | - Noriyoshi Manabe
- Division of Structural Glycobiology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, Sendai, Japan
| | - Yoshiki Yamaguchi
- Division of Structural Glycobiology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, Sendai, Japan
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3
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Kessler N, Akabayov SR, Cohen LS, Scherf T, Naider F, Anglister J. The chemokines CCL5 and CXCL12 exhibit high-affinity binding to N-terminal peptides of the non-cognate receptors CXCR4 and CCR5, respectively. FEBS J 2024; 291:458-476. [PMID: 37997026 DOI: 10.1111/febs.17013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/16/2023] [Accepted: 11/21/2023] [Indexed: 11/25/2023]
Abstract
CC and CXC chemokines are distinct chemokine subfamilies. CC chemokines usually do not bind CXC-chemokine receptors and vice versa. CCR5 and CXCR4 receptors are activated by CCL5 and CXCL12 chemokines, respectively, and are also used as HIV-1 coreceptors. CCL5 contains one conserved binding site for a sulfated tyrosine residue, whereas CXCL12 is unique in having two additional sites for sulfated/nonsulfated tyrosine residues. In this study, N-terminal (Nt) CXCR4 peptides were found to bind CCL5 with somewhat higher affinities in comparison to those of short Nt-CCR5(8-20) peptides with the same number of sulfated tyrosine residues. Similarly, a long Nt-CCR5(1-27)(s Y3,s Y10,s Y14) peptide cross reacts with CXCL12 and with lower KD in comparison to its binding to CCL5. Intermolecular nuclear overhauser effect (NOE) measurements were used to decipher the mechanism of the chemokine/Nt-receptor peptide binding. The Nt-CXCR4 peptides interact with the conserved CCL5 tyrosine sulfate-binding site by an allovalency mechanism like that observed for CCL5 binding of Nt-CCR5 peptides. Nt-CCR5 peptides bind CXCL12 in multiple modes analogous to their binding to HIV-1 gp120 and interact with all three tyrosine/sulfated tyrosine-binding pockets of CXCL12. We suggest that the chemokine-receptors Nt-segments bind promiscuously to cognate and non-cognate chemokines and in a mechanism that is dependent on the number of binding pockets for tyrosine residues found on the chemokine. In conclusion, common features shared among the chemokine-receptors' Nt-segments such as multiple tyrosine residues that are potentially sulfated, and a large number of negatively charged residues are the reason of the cross binding observed in this study.
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Affiliation(s)
- Naama Kessler
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sabine R Akabayov
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Leah S Cohen
- Department of Chemistry and Macromolecular Assembly Institute, College of Staten Island of the City University of New York, Staten Island, NY, USA
- The Ph.D. Programs in Biochemistry and Chemistry, The Graduate Center of the City University of New York, NY, USA
| | - Tali Scherf
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Fred Naider
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
- Department of Chemistry and Macromolecular Assembly Institute, College of Staten Island of the City University of New York, Staten Island, NY, USA
- The Ph.D. Programs in Biochemistry and Chemistry, The Graduate Center of the City University of New York, NY, USA
| | - Jacob Anglister
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
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4
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Šimek M, Nešporová K, Kocurková A, Foglová T, Ambrožová G, Velebný V, Kubala L, Hermannová M. How the molecular weight affects the in vivo fate of exogenous hyaluronan delivered intravenously: A stable-isotope labelling strategy. Carbohydr Polym 2021; 263:117927. [PMID: 33858586 DOI: 10.1016/j.carbpol.2021.117927] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/21/2021] [Accepted: 03/07/2021] [Indexed: 12/15/2022]
Abstract
There is inconsistent information regarding the size effects of exogenously given hyaluronan on its in vivo fate. The data are often biased by the poor quality of hyaluronan and non-ideal labelling strategies used for resolving exogenous/endogenous hyaluronan, which only monitor the label and not hyaluronan itself. To overcome these drawbacks and establish the pharmacokinetics of intravenous hyaluronan in relation to its Mw, 13C-labelled HA of five Mws from 13.6-1562 kDa was prepared and administered to mice at doses 25-50 mg kg-1. The elimination efficiency increased with decreasing Mw. Low Mw hyaluronan was rapidly eliminated as small hyaluronan fragments in urine, while high Mw hyaluronan exhibited saturable kinetics and complete metabolization within 48 h. All tested Mws exhibited a similar uptake by liver cells and metabolization into activated sugars. 13C-labelling combined with LC-MS provides an excellent approach to elucidating in vivo fate and biological activities of hyaluronan.
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Affiliation(s)
- Matěj Šimek
- Contipro a.s., Dolní Dobrouč 401, 56102, Dolní Dobrouč, Czech Republic; Department of Analytical Chemistry, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | | | - Anna Kocurková
- International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic; Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic; Institute of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Tereza Foglová
- Contipro a.s., Dolní Dobrouč 401, 56102, Dolní Dobrouč, Czech Republic
| | - Gabriela Ambrožová
- International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic; Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Vladimír Velebný
- Contipro a.s., Dolní Dobrouč 401, 56102, Dolní Dobrouč, Czech Republic
| | - Lukáš Kubala
- International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic; Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic; Institute of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic.
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5
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Künze G, Huster D, Samsonov SA. Investigation of the structure of regulatory proteins interacting with glycosaminoglycans by combining NMR spectroscopy and molecular modeling - the beginning of a wonderful friendship. Biol Chem 2021; 402:1337-1355. [PMID: 33882203 DOI: 10.1515/hsz-2021-0119] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 04/09/2021] [Indexed: 11/15/2022]
Abstract
The interaction of regulatory proteins with extracellular matrix or cell surface-anchored glycosaminoglycans (GAGs) plays important roles in molecular recognition, wound healing, growth, inflammation and many other processes. In spite of their high biological relevance, protein-GAG complexes are significantly underrepresented in structural databases because standard tools for structure determination experience difficulties in studying these complexes. Co-crystallization with subsequent X-ray analysis is hampered by the high flexibility of GAGs. NMR spectroscopy experiences difficulties related to the periodic nature of the GAGs and the sparse proton network between protein and GAG with distances that typically exceed the detection limit of nuclear Overhauser enhancement spectroscopy. In contrast, computer modeling tools have advanced over the last years delivering specific protein-GAG docking approaches successfully complemented with molecular dynamics (MD)-based analysis. Especially the combination of NMR spectroscopy in solution providing sparse structural constraints with molecular docking and MD simulations represents a useful synergy of forces to describe the structure of protein-GAG complexes. Here we review recent methodological progress in this field and bring up examples where the combination of new NMR methods along with cutting-edge modeling has yielded detailed structural information on complexes of highly relevant cytokines with GAGs.
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Affiliation(s)
- Georg Künze
- Center for Structural Biology, Vanderbilt University, 465 21st Ave S, 5140 MRB3, Nashville, TN37240, USA.,Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, TN37235, USA.,Institute for Drug Discovery, University of Leipzig, Brüderstr. 34, D-04103Leipzig, Germany
| | - Daniel Huster
- Institute for Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, D-04107Leipzig, Germany
| | - Sergey A Samsonov
- Faculty of Chemistry, University of Gdańsk, Ul. Wita Stwosza 63, 80-308Gdańsk, Poland
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6
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Bu C, Jin L. NMR Characterization of the Interactions Between Glycosaminoglycans and Proteins. Front Mol Biosci 2021; 8:646808. [PMID: 33796549 PMCID: PMC8007983 DOI: 10.3389/fmolb.2021.646808] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 02/24/2021] [Indexed: 12/16/2022] Open
Abstract
Glycosaminoglycans (GAGs) constitute a considerable fraction of the glycoconjugates found on cellular membranes and in the extracellular matrix of virtually all mammalian tissues. The essential role of GAG-protein interactions in the regulation of physiological processes has been recognized for decades. However, the underlying molecular basis of these interactions has only emerged since 1990s. The binding specificity of GAGs is encoded in their primary structures, but ultimately depends on how their functional groups are presented to a protein in the three-dimensional space. This review focuses on the application of NMR spectroscopy on the characterization of the GAG-protein interactions. Examples of interpretation of the complex mechanism and characterization of structural motifs involved in the GAG-protein interactions are given. Selected families of GAG-binding proteins investigated using NMR are also described.
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Affiliation(s)
- Changkai Bu
- National Glycoengineering Research Center, Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, China
| | - Lan Jin
- National Glycoengineering Research Center, Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, China
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7
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Préchoux A, Simorre JP, Lortat-Jacob H, Laguri C. Deciphering the structural attributes of protein-heparan sulfate interactions using chemo-enzymatic approaches and NMR spectroscopy. Glycobiology 2021; 31:851-858. [PMID: 33554262 DOI: 10.1093/glycob/cwab012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/18/2020] [Accepted: 01/28/2021] [Indexed: 11/14/2022] Open
Abstract
Heparan sulfates (HS) is a polysaccharide found at the cell surface, where it mediates interactions with hundreds of proteins and regulates major pathophysiological processes. HS is highly heterogeneous and structurally complex and examples that define their structure-activity relationships remain limited. Here, to characterize a protein-HS interface and define the corresponding saccharide binding domain, we present a chemoenzymatic approach that generate 13C labeled HS-based oligosaccharide structures. NMR spectroscopy that efficiently discriminates between important or redundant chemical groups in the oligosaccharides, is employed to characterize these molecules alone and in interaction with proteins. Using chemokines as model system, docking based on NMR data on both proteins and oligosaccharides enable the identification of the structural determinant involved in the complex. This study shows that both the position of the sulfo-groups along the chain and their mode of presentation, rather than their overall number, are key determinant and further points out the usefulness of these 13C labeled oligosaccharides in obtaining detailed structural information on HS-protein complexes.
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Affiliation(s)
| | | | | | - Cédric Laguri
- Univ. Grenoble Alpes, CNRS, CEA, IBS, F-38000 Grenoble
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8
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Quantitative analysis of heparan sulfate using isotopically labeled calibrants. Commun Biol 2020; 3:425. [PMID: 32753592 PMCID: PMC7403576 DOI: 10.1038/s42003-020-01150-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 07/06/2020] [Indexed: 12/14/2022] Open
Abstract
Heparan sulfate is a sulfated polysaccharide that displays essential physiological functions. Here, we report a LC-MS/MS-based method for quantitatively determining the individual disaccharide composition and total amount of heparan sulfate. Using eight 13C-labeled disaccharide calibrants and one 13C-labeled polysaccharide calibrant, we complete the analysis in one-pot process. The method is both sensitive and has the throughput to analyze heparan sulfate from mouse tissues and plasma. Wang et al. describe a strategy for quantitatively performing composition analysis of heparan sulfate using 13C-labeled disaccharides and polysaccharides that mimic the glycosaminoglycan chemical structure. They further show that these isotopically labelled small molecules can be used as internal standards for mass spectrometry analysis of heparan sulfate derived from mouse tissue and plasma.
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9
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Wang H, Zhang L, Wang Y, Li J, Du G, Kang Z. Engineering the heparin-binding pocket to enhance the catalytic efficiency of a thermostable heparinase III from Bacteroides thetaiotaomicron. Enzyme Microb Technol 2020; 137:109549. [DOI: 10.1016/j.enzmictec.2020.109549] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 02/26/2020] [Accepted: 03/08/2020] [Indexed: 02/06/2023]
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10
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Vignovich WP, Pomin VH. Saturation Transfer Difference in Characterization of Glycosaminoglycan-Protein Interactions. SLAS Technol 2020; 25:307-319. [PMID: 32452261 DOI: 10.1177/2472630320921130] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Novel methods in nuclear magnetic resonance (NMR) spectroscopy have recently been developed to investigate the binding properties of intermolecular complexes endowed with biomedical functions. Among these methods is the saturation transfer difference (STD), which enables the mapping of specific binding motifs of functional ligands. STD can efficiently uncover the specific and preferential binding sites of these ligands in their intermolecular complexes. This is particularly useful in the case of glycosaminoglycans (GAGs), a group of sulfated polysaccharides that play pivotal roles in various biological and pathological processes. The activity of GAGs is ultimately mediated through molecular interactions with key functional proteins, namely, GAG-binding proteins (GBPs). The quality of the GAG-GBP interactions depends on sulfation patterns, oligosaccharide length, and the composing monosaccharides of GAGs. Through STD NMR, information about the atoms of the GAG ligands involved in the complexes is provided. Here we highlight the latest achievements of the literature using STD NMR on GAG oligosaccharide-GBP complexes. Interestingly, most of the GBPs studied so far by STD NMR belong to one of the three major classes: coagulation factors, growth factors, or chemokine/cytokines. Unveiling the structural requirements of GAG ligands in bindings with their protein partners is a crucial step to understand the biochemical and medical actions of GAGs. This process is also a requirement in GAG-based drug discovery and development.
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Affiliation(s)
- William P Vignovich
- BioMolecular Sciences Department, School of Pharmacy, the University of Mississippi, Oxford, MS, USA
| | - Vitor H Pomin
- BioMolecular Sciences Department, School of Pharmacy, the University of Mississippi, Oxford, MS, USA.,Research Institute of Pharmaceutical Sciences, School of Pharmacy, the University of Mississippi, Oxford, MS, USA
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11
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Spiller S, Panitz N, Limasale YDP, Atallah PM, Schirmer L, Bellmann-Sickert K, Blaszkiewicz J, Koehling S, Freudenberg U, Rademann J, Werner C, Beck-Sickinger AG. Modulation of Human CXCL12 Binding Properties to Glycosaminoglycans To Enhance Chemotactic Gradients. ACS Biomater Sci Eng 2019; 5:5128-5138. [DOI: 10.1021/acsbiomaterials.9b01139] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Sabrina Spiller
- Universität Leipzig, Faculty of Life Sciences, Institute of Biochemistry, Brüderstrasse 34, 04103 Leipzig, Germany
| | - Nydia Panitz
- Universität Leipzig, Faculty of Life Sciences, Institute of Biochemistry, Brüderstrasse 34, 04103 Leipzig, Germany
| | - Yanuar Dwi Putra Limasale
- Leibniz Institute of Polymer Research Dresden (IPF), Max Bergmann Center of Biomaterials Dresden (MBC), Hohe Strasse 6, 01069 Dresden, Germany
| | - Passant Morsi Atallah
- Leibniz Institute of Polymer Research Dresden (IPF), Max Bergmann Center of Biomaterials Dresden (MBC), Hohe Strasse 6, 01069 Dresden, Germany
| | - Lucas Schirmer
- Leibniz Institute of Polymer Research Dresden (IPF), Max Bergmann Center of Biomaterials Dresden (MBC), Hohe Strasse 6, 01069 Dresden, Germany
| | - Kathrin Bellmann-Sickert
- Universität Leipzig, Faculty of Life Sciences, Institute of Biochemistry, Brüderstrasse 34, 04103 Leipzig, Germany
| | - Joanna Blaszkiewicz
- Freie Universität Berlin, Medicinal Chemistry, Königin-Luise-Strasse 2+4, Berlin 14195, Germany
| | - Sebastian Koehling
- Freie Universität Berlin, Medicinal Chemistry, Königin-Luise-Strasse 2+4, Berlin 14195, Germany
| | - Uwe Freudenberg
- Leibniz Institute of Polymer Research Dresden (IPF), Max Bergmann Center of Biomaterials Dresden (MBC), Hohe Strasse 6, 01069 Dresden, Germany
| | - Jörg Rademann
- Freie Universität Berlin, Medicinal Chemistry, Königin-Luise-Strasse 2+4, Berlin 14195, Germany
| | - Carsten Werner
- Leibniz Institute of Polymer Research Dresden (IPF), Max Bergmann Center of Biomaterials Dresden (MBC), Hohe Strasse 6, 01069 Dresden, Germany
| | - Annette G. Beck-Sickinger
- Universität Leipzig, Faculty of Life Sciences, Institute of Biochemistry, Brüderstrasse 34, 04103 Leipzig, Germany
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12
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Glycosaminoglycan-Protein Interactions by Nuclear Magnetic Resonance (NMR) Spectroscopy. Molecules 2018; 23:molecules23092314. [PMID: 30208595 PMCID: PMC6225283 DOI: 10.3390/molecules23092314] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 08/29/2018] [Accepted: 09/05/2018] [Indexed: 02/07/2023] Open
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is one of the most utilized and informative analytical techniques for investigating glycosaminoglycan (GAG)-protein complexes. NMR methods that are commonly applied to GAG-protein systems include chemical shift perturbation, saturation transfer difference, and transferred nuclear Overhauser effect. Although these NMR methods have revealed valuable insight into the protein-GAG complexes, elucidating high-resolution structural and dynamic information of these often transient interactions remains challenging. In addition, preparation of structurally homogeneous and isotopically enriched GAG ligands for structural investigations continues to be laborious. As a result, understanding of the structure-activity relationship of GAGs is still primitive. To overcome these deficiencies, several innovative NMR techniques have been developed lately. Here, we review some of the commonly used techniques along with more novel methods such as waterLOGSY and experiments to examine structure and dynamic of lysine and arginine side chains to identify GAG-binding sites. We will also present the latest technology that is used to produce isotopically enriched as well as paramagnetically tagged GAG ligands. Recent results that were obtained from solid-state NMR of amyloid’s interaction with GAG are also presented together with a brief discussion on computer assisted modeling of GAG-protein complexes using sparse experimental data.
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13
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Karamanos NK, Piperigkou Z, Theocharis AD, Watanabe H, Franchi M, Baud S, Brézillon S, Götte M, Passi A, Vigetti D, Ricard-Blum S, Sanderson RD, Neill T, Iozzo RV. Proteoglycan Chemical Diversity Drives Multifunctional Cell Regulation and Therapeutics. Chem Rev 2018; 118:9152-9232. [DOI: 10.1021/acs.chemrev.8b00354] [Citation(s) in RCA: 193] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Nikos K. Karamanos
- Biochemistry, Biochemical Analysis & Matrix Pathobiology Research Group, Laboratory of Biochemistry, Department of Chemistry, University of Patras, Patras 26110, Greece
- Foundation for Research and Technology-Hellas (FORTH)/Institute of Chemical Engineering Sciences (ICE-HT), Patras 26110, Greece
| | - Zoi Piperigkou
- Biochemistry, Biochemical Analysis & Matrix Pathobiology Research Group, Laboratory of Biochemistry, Department of Chemistry, University of Patras, Patras 26110, Greece
- Foundation for Research and Technology-Hellas (FORTH)/Institute of Chemical Engineering Sciences (ICE-HT), Patras 26110, Greece
| | - Achilleas D. Theocharis
- Biochemistry, Biochemical Analysis & Matrix Pathobiology Research Group, Laboratory of Biochemistry, Department of Chemistry, University of Patras, Patras 26110, Greece
| | - Hideto Watanabe
- Institute for Molecular Science of Medicine, Aichi Medical University, Aichi 480-1195, Japan
| | - Marco Franchi
- Department for Life Quality Studies, University of Bologna, Rimini 47100, Italy
| | - Stéphanie Baud
- Université de Reims Champagne-Ardenne, Laboratoire SiRMa, CNRS UMR MEDyC 7369, Faculté de Médecine, 51 rue Cognacq Jay, Reims 51100, France
| | - Stéphane Brézillon
- Université de Reims Champagne-Ardenne, Laboratoire de Biochimie Médicale et Biologie Moléculaire, CNRS UMR MEDyC 7369, Faculté de Médecine, 51 rue Cognacq Jay, Reims 51100, France
| | - Martin Götte
- Department of Gynecology and Obstetrics, Münster University Hospital, Münster 48149, Germany
| | - Alberto Passi
- Department of Medicine and Surgery, University of Insubria, Varese 21100, Italy
| | - Davide Vigetti
- Department of Medicine and Surgery, University of Insubria, Varese 21100, Italy
| | - Sylvie Ricard-Blum
- University Claude Bernard Lyon 1, CNRS, UMR 5246, Institute of Molecular and Supramolecular Chemistry and Biochemistry, Villeurbanne 69622, France
| | - Ralph D. Sanderson
- Department of Pathology, Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
| | - Thomas Neill
- Department of Pathology, Anatomy and Cell Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania 10107, United States
| | - Renato V. Iozzo
- Department of Pathology, Anatomy and Cell Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania 10107, United States
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14
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Pomin VH, Wang X. Synthetic Oligosaccharide Libraries and Microarray Technology: A Powerful Combination for the Success of Current Glycosaminoglycan Interactomics. ChemMedChem 2018; 13:648-661. [PMID: 29160016 PMCID: PMC5895483 DOI: 10.1002/cmdc.201700620] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 11/15/2017] [Indexed: 11/08/2022]
Abstract
Glycosaminoglycans (GAGs) are extracellular matrix and/or cell-surface sulfated glycans crucial to the regulation of various signaling proteins, the functions of which are essential in many pathophysiological systems. Because structural heterogeneity is high in GAG chains and purification is difficult, the use of structurally defined GAG oligosaccharides from natural sources as molecular models in both biophysical and pharmacological assays is limited. To overcome this obstacle, GAG-like oligosaccharides of well-defined structures are currently being synthesized by chemical and/or enzymatic means in many research groups around the world. These synthetic GAG oligosaccharides serve as useful molecular tools in studies of GAG-protein interactions. In this review, besides discussing the commonest routes used for the synthesis of GAG oligosaccharides, we also survey some libraries of these synthetic models currently available for research and discuss their activities in interaction studies with functional proteins, especially through the microarray approach.
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Affiliation(s)
- Vitor H Pomin
- Program of Glycobiology, Institute of Medical Biochemistry Leopoldo de Meis and University Hospital Clementino Fraga Filho, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-913, Brazil
| | - Xu Wang
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
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15
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Hu G, Shao M, Gao X, Wang F, Liu C. Probing cleavage promiscuity of heparinase III towards chemoenzymatically synthetic heparan sulfate oligosaccharides. Carbohydr Polym 2017; 173:276-285. [DOI: 10.1016/j.carbpol.2017.05.071] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/10/2017] [Accepted: 05/23/2017] [Indexed: 01/07/2023]
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16
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Schubert M. Insights into Carbohydrate Recognition by 3D Structure Determination of Protein–Carbohydrate Complexes Using NMR. NMR IN GLYCOSCIENCE AND GLYCOTECHNOLOGY 2017:101-122. [DOI: 10.1039/9781782623946-00101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
This chapter provides an overview of protein–carbohydrate complex structures determined with NMR spectroscopy and deposited in the Protein Data Bank (PDB). These 14 structures include protein–carbohydrate interactions ranging from nanomolar to millimolar affinities. Two complexes are discussed in detail, one representing a tightly bound complex and one a weak but specific interaction. This review illustrates that NMR spectroscopy is a competitive method for three-dimensional structure determination of protein–carbohydrate complexes, especially in the case of weak interactions. The number of biological functions in which protein–carbohydrate interactions are involved is steadily growing. Essential functions of the immune system such as the distinction between self and non-self, or the resolution of inflammation, involve critical protein–carbohydrate recognition events. It is therefore expected that by providing atomic details, NMR spectroscopy can make a significant contribution in the near future to unexplored pathways of the immune system and of many other biological processes.
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Affiliation(s)
- Mario Schubert
- Department of Molecular Biology, University of Salzburg 5020 Salzburg Austria
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17
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Thakar D, Dalonneau F, Migliorini E, Lortat-Jacob H, Boturyn D, Albiges-Rizo C, Coche-Guerente L, Picart C, Richter RP. Binding of the chemokine CXCL12α to its natural extracellular matrix ligand heparan sulfate enables myoblast adhesion and facilitates cell motility. Biomaterials 2017; 123:24-38. [PMID: 28152381 PMCID: PMC5405871 DOI: 10.1016/j.biomaterials.2017.01.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 01/04/2017] [Accepted: 01/17/2017] [Indexed: 01/24/2023]
Abstract
The chemokine CXCL12α is a potent chemoattractant that guides the migration of muscle precursor cells (myoblasts) during myogenesis and muscle regeneration. To study how the molecular presentation of chemokines influences myoblast adhesion and motility, we designed multifunctional biomimetic surfaces as a tuneable signalling platform that enabled the response of myoblasts to selected extracellular cues to be studied in a well-defined environment. Using this platform, we demonstrate that CXCL12α, when presented by its natural extracellular matrix ligand heparan sulfate (HS), enables the adhesion and spreading of myoblasts and facilitates their active migration. In contrast, myoblasts also adhered and spread on CXCL12α that was quasi-irreversibly surface-bound in the absence of HS, but were essentially immotile. Moreover, co-presentation of the cyclic RGD peptide as integrin ligand along with HS-bound CXCL12α led to enhanced spreading and motility, in a way that indicates cooperation between CXCR4 (the CXCL12α receptor) and integrins (the RGD receptors). Our findings reveal the critical role of HS in CXCL12α induced myoblast adhesion and migration. The biomimetic surfaces developed here hold promise for mechanistic studies of cellular responses to different presentations of biomolecules. They may be broadly applicable for dissecting the signalling pathways underlying receptor cross-talks, and thus may guide the development of novel biomaterials that promote highly specific cellular responses.
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Affiliation(s)
- Dhruv Thakar
- Université Grenoble Alpes, Département de Chimie Moléculaire (DCM), Grenoble, France; CNRS, DCM, Grenoble, France
| | - Fabien Dalonneau
- CNRS UMR 5628 (LMGP), Grenoble, France; Grenoble Institute of Technology, Université Grenoble Alpes, LMGP, Grenoble, France
| | - Elisa Migliorini
- Université Grenoble Alpes, Département de Chimie Moléculaire (DCM), Grenoble, France; CNRS, DCM, Grenoble, France
| | - Hugues Lortat-Jacob
- Institut de Biologie Structurale, UMR 5075, Université Grenoble Alpes, CNRS, CEA, Grenoble, France
| | - Didier Boturyn
- Université Grenoble Alpes, Département de Chimie Moléculaire (DCM), Grenoble, France; CNRS, DCM, Grenoble, France
| | - Corinne Albiges-Rizo
- Institut Albert Bonniot, Université Grenoble Alpes, INSERM, CNRS, Grenoble, France
| | - Liliane Coche-Guerente
- Université Grenoble Alpes, Département de Chimie Moléculaire (DCM), Grenoble, France; CNRS, DCM, Grenoble, France
| | - Catherine Picart
- CNRS UMR 5628 (LMGP), Grenoble, France; Grenoble Institute of Technology, Université Grenoble Alpes, LMGP, Grenoble, France.
| | - Ralf P Richter
- Université Grenoble Alpes, Département de Chimie Moléculaire (DCM), Grenoble, France; CNRS, DCM, Grenoble, France; University of Leeds, School of Biomedical Sciences and School of Physics and Astronomy, Leeds, United Kingdom; CIC biomaGUNE, San Sebastian, Spain.
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18
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Collins PJ, McCully ML, Martínez-Muñoz L, Santiago C, Wheeldon J, Caucheteux S, Thelen S, Cecchinato V, Laufer JM, Purvanov V, Monneau YR, Lortat-Jacob H, Legler DF, Uguccioni M, Thelen M, Piguet V, Mellado M, Moser B. Epithelial chemokine CXCL14 synergizes with CXCL12 via allosteric modulation of CXCR4. FASEB J 2017; 31:3084-3097. [PMID: 28360196 PMCID: PMC5472405 DOI: 10.1096/fj.201700013r] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 03/13/2017] [Indexed: 12/02/2022]
Abstract
The chemokine receptor, CXC chemokine receptor 4 (CXCR4), is selective for CXC chemokine ligand 12 (CXCL12), is broadly expressed in blood and tissue cells, and is essential during embryogenesis and hematopoiesis. CXCL14 is a homeostatic chemokine with unknown receptor selectivity and preferential expression in peripheral tissues. Here, we demonstrate that CXCL14 synergized with CXCL12 in the induction of chemokine responses in primary human lymphoid cells and cell lines that express CXCR4. Combining subactive concentrations of CXCL12 with 100–300 nM CXCL14 resulted in chemotaxis responses that exceeded maximal responses that were obtained with CXCL12 alone. CXCL14 did not activate CXCR4-expressing cells (i.e., failed to trigger chemotaxis and Ca2+ mobilization, as well as signaling via ERK1/2 and the small GTPase Rac1); however, CXCL14 bound to CXCR4 with high affinity, induced redistribution of cell-surface CXCR4, and enhanced HIV-1 infection by >3-fold. We postulate that CXCL14 is a positive allosteric modulator of CXCR4 that enhances the potency of CXCR4 ligands. Our findings provide new insights that will inform the development of novel therapeutics that target CXCR4 in a range of diseases, including cancer, autoimmunity, and HIV.—Collins, P. J., McCully, M. L., Martínez-Muñoz, L., Santiago, C., Wheeldon, J., Caucheteux, S., Thelen, S., Cecchinato, V., Laufer, J. M., Purvanov, V., Monneau, Y. R., Lortat-Jacob, H., Legler, D. F., Uguccioni, M., Thelen, M., Piguet, V., Mellado, M., Moser, B. Epithelial chemokine CXCL14 synergizes with CXCL12 via allosteric modulation of CXCR4.
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Affiliation(s)
- Paul J Collins
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Michelle L McCully
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Laura Martínez-Muñoz
- Department Immunology and Oncology, Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - César Santiago
- Department Immunology and Oncology, Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - James Wheeldon
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Stephan Caucheteux
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Sylvia Thelen
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Valentina Cecchinato
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Julia M Laufer
- Biotechnology Institute Thurgau at the University of Konstanz, Kreuzlingen, Switzerland.,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Vladimir Purvanov
- Biotechnology Institute Thurgau at the University of Konstanz, Kreuzlingen, Switzerland.,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Yoan R Monneau
- Institute de Biologie Structurale, Unité Mixtes de Recherche 5075, University Grenoble Alpes, Centre National de la Recherche Scientifique, Commissariat à l'Énergie Atomique, Grenoble, France
| | - Hugues Lortat-Jacob
- Institute de Biologie Structurale, Unité Mixtes de Recherche 5075, University Grenoble Alpes, Centre National de la Recherche Scientifique, Commissariat à l'Énergie Atomique, Grenoble, France
| | - Daniel F Legler
- Biotechnology Institute Thurgau at the University of Konstanz, Kreuzlingen, Switzerland.,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Mariagrazia Uguccioni
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland.,Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy
| | - Marcus Thelen
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Vincent Piguet
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Mario Mellado
- Department Immunology and Oncology, Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Bernhard Moser
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom;
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19
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Mulloy B, Hogwood J, Gray E, Lever R, Page CP. Pharmacology of Heparin and Related Drugs. Pharmacol Rev 2016; 68:76-141. [PMID: 26672027 DOI: 10.1124/pr.115.011247] [Citation(s) in RCA: 216] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Heparin has been recognized as a valuable anticoagulant and antithrombotic for several decades and is still widely used in clinical practice for a variety of indications. The anticoagulant activity of heparin is mainly attributable to the action of a specific pentasaccharide sequence that acts in concert with antithrombin, a plasma coagulation factor inhibitor. This observation has led to the development of synthetic heparin mimetics for clinical use. However, it is increasingly recognized that heparin has many other pharmacological properties, including but not limited to antiviral, anti-inflammatory, and antimetastatic actions. Many of these activities are independent of its anticoagulant activity, although the mechanisms of these other activities are currently less well defined. Nonetheless, heparin is being exploited for clinical uses beyond anticoagulation and developed for a wide range of clinical disorders. This article provides a "state of the art" review of our current understanding of the pharmacology of heparin and related drugs and an overview of the status of development of such drugs.
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Affiliation(s)
- Barbara Mulloy
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (B.M., C.P.P.); National Institute for Biological Standards and Control, Potters Bar, Hertfordshire, United Kingdom (J.H., E.G.); and University College London School of Pharmacy, London, United Kingdom (R.L.)
| | - John Hogwood
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (B.M., C.P.P.); National Institute for Biological Standards and Control, Potters Bar, Hertfordshire, United Kingdom (J.H., E.G.); and University College London School of Pharmacy, London, United Kingdom (R.L.)
| | - Elaine Gray
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (B.M., C.P.P.); National Institute for Biological Standards and Control, Potters Bar, Hertfordshire, United Kingdom (J.H., E.G.); and University College London School of Pharmacy, London, United Kingdom (R.L.)
| | - Rebecca Lever
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (B.M., C.P.P.); National Institute for Biological Standards and Control, Potters Bar, Hertfordshire, United Kingdom (J.H., E.G.); and University College London School of Pharmacy, London, United Kingdom (R.L.)
| | - Clive P Page
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (B.M., C.P.P.); National Institute for Biological Standards and Control, Potters Bar, Hertfordshire, United Kingdom (J.H., E.G.); and University College London School of Pharmacy, London, United Kingdom (R.L.)
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20
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Panitz N, Theisgen S, Samsonov SA, Gehrcke JP, Baumann L, Bellmann-Sickert K, Köhling S, Pisabarro MT, Rademann J, Huster D, Beck-Sickinger AG. The structural investigation of glycosaminoglycan binding to CXCL12 displays distinct interaction sites. Glycobiology 2016; 26:1209-1221. [DOI: 10.1093/glycob/cww059] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Revised: 05/15/2016] [Accepted: 05/15/2016] [Indexed: 12/14/2022] Open
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21
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Migliorini E, Thakar D, Kühnle J, Sadir R, Dyer DP, Li Y, Sun C, Volkman BF, Handel TM, Coche-Guerente L, Fernig DG, Lortat-Jacob H, Richter RP. Cytokines and growth factors cross-link heparan sulfate. Open Biol 2016; 5:rsob.150046. [PMID: 26269427 PMCID: PMC4554917 DOI: 10.1098/rsob.150046] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The glycosaminoglycan heparan sulfate (HS), present at the surface of most cells and ubiquitous in extracellular matrix, binds many soluble extracellular signalling molecules such as chemokines and growth factors, and regulates their transport and effector functions. It is, however, unknown whether upon binding HS these proteins can affect the long-range structure of HS. To test this idea, we interrogated a supramolecular model system, in which HS chains grafted to streptavidin-functionalized oligoethylene glycol monolayers or supported lipid bilayers mimic the HS-rich pericellular or extracellular matrix, with the biophysical techniques quartz crystal microbalance (QCM-D) and fluorescence recovery after photobleaching (FRAP). We were able to control and characterize the supramolecular presentation of HS chains—their local density, orientation, conformation and lateral mobility—and their interaction with proteins. The chemokine CXCL12α (or SDF-1α) rigidified the HS film, and this effect was due to protein-mediated cross-linking of HS chains. Complementary measurements with CXCL12α mutants and the CXCL12γ isoform provided insight into the molecular mechanism underlying cross-linking. Fibroblast growth factor 2 (FGF-2), which has three HS binding sites, was also found to cross-link HS, but FGF-9, which has just one binding site, did not. Based on these data, we propose that the ability to cross-link HS is a generic feature of many cytokines and growth factors, which depends on the architecture of their HS binding sites. The ability to change matrix organization and physico-chemical properties (e.g. permeability and rigidification) implies that the functions of cytokines and growth factors may not simply be confined to the activation of cognate cellular receptors.
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Affiliation(s)
- Elisa Migliorini
- Université Grenoble Alpes, Departement de Chimie Moléculaire (DCM), Grenoble, France CNRS, DCM, Grenoble, France CIC biomaGUNE, San Sebastian, Spain
| | - Dhruv Thakar
- Université Grenoble Alpes, Departement de Chimie Moléculaire (DCM), Grenoble, France CNRS, DCM, Grenoble, France
| | - Jens Kühnle
- Department of Biophysical Chemistry, University of Heidelberg, Heidelberg, Germany
| | - Rabia Sadir
- Université Grenoble Alpes, Institut de Biologie Structurale (IBS), Grenoble, France CNRS, IBS, Grenoble, France CEA, IBS, Grenoble, France
| | - Douglas P Dyer
- University of California, San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA, USA
| | - Yong Li
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Changye Sun
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Brian F Volkman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Tracy M Handel
- University of California, San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA, USA
| | - Liliane Coche-Guerente
- Université Grenoble Alpes, Departement de Chimie Moléculaire (DCM), Grenoble, France CNRS, DCM, Grenoble, France
| | - David G Fernig
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Hugues Lortat-Jacob
- Université Grenoble Alpes, Institut de Biologie Structurale (IBS), Grenoble, France CNRS, IBS, Grenoble, France CEA, IBS, Grenoble, France
| | - Ralf P Richter
- Université Grenoble Alpes, Departement de Chimie Moléculaire (DCM), Grenoble, France CNRS, DCM, Grenoble, France CIC biomaGUNE, San Sebastian, Spain Max Planck Institute for Intelligent Systems, Stuttgart, Germany
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22
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Monneau Y, Arenzana-Seisdedos F, Lortat-Jacob H. The sweet spot: how GAGs help chemokines guide migrating cells. J Leukoc Biol 2015; 99:935-53. [DOI: 10.1189/jlb.3mr0915-440r] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Accepted: 11/24/2015] [Indexed: 12/19/2022] Open
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23
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Yuan H, Ying J, Deng P, Chen P, Shi J, Liu Y, Gao X, Zhao Y. Specific interactions of leucine with disaccharides by electrospray ionization mass spectrometry: application to rapid differentiation of disaccharide isomers in combination with statistical analysis. Analyst 2015; 140:7965-73. [PMID: 26514183 DOI: 10.1039/c5an01735a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The identification of carbohydrate isomers, including mono units, linkage positions and anomeric configurations, remains an arduous subject. In this study, the natural amino acid leucine (Leu) was found to specifically interact with cellobiose (Cello) to form a series of potassium adducts as [Cello + Leu + K](+), [Cello + 2Leu + K](+), and [2Cello + Leu + K](+) in the gas phase using mass spectrometry. By using CID-MS/MS, these complexes produced specific fragmentation patterns from the sugar backbone cleavage instead of non-covalent interactions. Moreover, their fragment distributions were dependent on the ratios of Cello-to-Leu in the complexes and the fragmentation pathways of potassium-cationized disaccharides (Dis) were remarkably changed with leucine binding. It should be pointed out that the ternary complex [2Cello + AA + K](+) was unique for leucine among all the twenty natural amino acids. The [2Dis + Leu + K](+) complex produced the most informative fragments by tandem mass spectrometry, which was successfully applied for rapid and efficient discrimination of twelve glucose-containing disaccharide isomers in combination with statistical analyses including PCA and OPLS-DA. The methodology developed here not only provides a novel analytical approach for the differentiation of disaccharide isomers, but also brings new sight towards the interactions of amino acids with disaccharides.
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Affiliation(s)
- Hang Yuan
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, Key Laboratory for Chemical Biology of Fujian Province, Xiamen University, Xiamen, Fujian 361005, China.
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24
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Mechanistic and therapeutic overview of glycosaminoglycans: the unsung heroes of biomolecular signaling. Glycoconj J 2015; 33:1-17. [DOI: 10.1007/s10719-015-9642-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 11/19/2015] [Accepted: 11/20/2015] [Indexed: 12/28/2022]
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25
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Pomin VH, Mulloy B. Current structural biology of the heparin interactome. Curr Opin Struct Biol 2015; 34:17-25. [PMID: 26038285 DOI: 10.1016/j.sbi.2015.05.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 05/03/2015] [Accepted: 05/12/2015] [Indexed: 10/23/2022]
Abstract
Heparin is the best known therapeutically active carbohydrate. It can bind and regulate multiple functional proteins such as coagulation cofactors, chemokines, and growth factors. This versatility has led to the recently developed concept of the heparin interactome--a group of proteins that, as the name implies, interact with heparin. The heparin interactome is structurally and functionally diverse. Though natural ligands of this class of proteins may be any of the glycosaminoglycans however, their structural biology is generally studied using heparin as a model compound. NMR spectroscopy contributes significantly to structural investigations of the resultant complexes in solution. This review aims therefore at discussing the current status in structural biology of the molecular complexes formed between heparin and its protein partners through the current concept of the heparin interactome.
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Affiliation(s)
- Vitor H Pomin
- Program of Glycobiology, Institute of Medical Biochemistry Leopoldo de Meis, and University Hospital Clementino Fraga Filho, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-913, Brazil.
| | - Barbara Mulloy
- Glycosciences Laboratory, Imperial College, Department of Medicine, Burlington Danes Building, Du Cane Road, London W12 0NN, UK.
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26
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Préchoux A, Halimi C, Simorre JP, Lortat-Jacob H, Laguri C. C5-epimerase and 2-O-sulfotransferase associate in vitro to generate contiguous epimerized and 2-O-sulfated heparan sulfate domains. ACS Chem Biol 2015; 10:1064-71. [PMID: 25594747 DOI: 10.1021/cb501037a] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Heparan sulfate (HS), a complex polysaccharide of the cell surface, is endowed with the remarkable ability to bind numerous proteins and, as such, regulates a large variety of biological processes. Protein binding depends on HS structure; however, in the absence of a template driving its biosynthesis, the mechanism by which protein binding sequences are assembled remains poorly known. Here, we developed a chemically defined 13C-labeled substrate and NMR based experiments to simultaneously follow in real time the activity of HS biosynthetic enzymes and characterize the reaction products. Using this new approach, we report that the association of C5-epimerase and 2-O-sulfotransferase, which catalyze the production of iduronic acid and its 2-O-sulfation, respectively, is necessary to processively generate extended sequences of contiguous IdoA2S-containing disaccharides, whereas modifications are randomly introduced when the enzymes are uncoupled. These data shed light on the mechanisms by which HS motifs are generated during biosynthesis. They support the view that HS structure assembly is controlled not only by the availability of the biosynthetic enzymes but also by their physical association, which in the case of the C5-epimerase and 2-O-sulfotransferase was characterized by an affinity of 80 nM as demonstrated by surface plasmon resonance experiments.
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Affiliation(s)
- Aurélie Préchoux
- Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38027 Grenoble, France
- CNRS, IBS, F-38027 Grenoble, France
- CEA, DSV, IBS, F-38027 Grenoble, France
| | - Célia Halimi
- Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38027 Grenoble, France
- CNRS, IBS, F-38027 Grenoble, France
- CEA, DSV, IBS, F-38027 Grenoble, France
| | - Jean-Pierre Simorre
- Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38027 Grenoble, France
- CNRS, IBS, F-38027 Grenoble, France
- CEA, DSV, IBS, F-38027 Grenoble, France
| | - Hugues Lortat-Jacob
- Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38027 Grenoble, France
- CNRS, IBS, F-38027 Grenoble, France
- CEA, DSV, IBS, F-38027 Grenoble, France
| | - Cédric Laguri
- Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38027 Grenoble, France
- CNRS, IBS, F-38027 Grenoble, France
- CEA, DSV, IBS, F-38027 Grenoble, France
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27
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Schanda P, Triboulet S, Laguri C, Bougault CM, Ayala I, Callon M, Arthur M, Simorre JP. Atomic model of a cell-wall cross-linking enzyme in complex with an intact bacterial peptidoglycan. J Am Chem Soc 2014; 136:17852-60. [PMID: 25429710 PMCID: PMC4544747 DOI: 10.1021/ja5105987] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The maintenance of bacterial cell shape and integrity is largely attributed to peptidoglycan, a highly cross-linked biopolymer. The transpeptidases that perform this cross-linking are important targets for antibiotics. Despite this biomedical importance, to date no structure of a protein in complex with an intact bacterial peptidoglycan has been resolved, primarily due to the large size and flexibility of peptidoglycan sacculi. Here we use solid-state NMR spectroscopy to derive for the first time an atomic model of an l,d-transpeptidase from Bacillus subtilis bound to its natural substrate, the intact B. subtilis peptidoglycan. Importantly, the model obtained from protein chemical shift perturbation data shows that both domains-the catalytic domain as well as the proposed peptidoglycan recognition domain-are important for the interaction and reveals a novel binding motif that involves residues outside of the classical enzymatic pocket. Experiments on mutants and truncated protein constructs independently confirm the binding site and the implication of both domains. Through measurements of dipolar-coupling derived order parameters of bond motion we show that protein binding reduces the flexibility of peptidoglycan. This first report of an atomic model of a protein-peptidoglycan complex paves the way for the design of new antibiotic drugs targeting l,d-transpeptidases. The strategy developed here can be extended to the study of a large variety of enzymes involved in peptidoglycan morphogenesis.
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Affiliation(s)
- Paul Schanda
- Univ. Grenoble Alpes, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
| | - Sébastien Triboulet
- Centre de Recherche des Cordeliers, LRMA, Equipe 12, Univ. Pierre et Marie Curie-Paris 6, UMR S 1138, 75006 Paris (France)
- Université Paris Descartes, Sorbonne, UMR S 1138, 75006 Paris (France); INSERM, U1138, 75006 Paris (France)
| | - Cédric Laguri
- Univ. Grenoble Alpes, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
| | - Catherine M. Bougault
- Univ. Grenoble Alpes, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
| | - Isabel Ayala
- Univ. Grenoble Alpes, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
| | - Morgane Callon
- Univ. Grenoble Alpes, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
| | - Michel Arthur
- Centre de Recherche des Cordeliers, LRMA, Equipe 12, Univ. Pierre et Marie Curie-Paris 6, UMR S 1138, 75006 Paris (France)
- Université Paris Descartes, Sorbonne, UMR S 1138, 75006 Paris (France); INSERM, U1138, 75006 Paris (France)
| | - Jean-Pierre Simorre
- Univ. Grenoble Alpes, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
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Well-defined biomimetic surfaces to characterize glycosaminoglycan-mediated interactions on the molecular, supramolecular and cellular levels. Biomaterials 2014; 35:8903-15. [DOI: 10.1016/j.biomaterials.2014.07.017] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 07/10/2014] [Indexed: 12/12/2022]
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Pomin VH. Biological findings from the recent NMR-based studies of glycosaminoglycan-protein interactions. Glycobiology 2014; 24:991-1003. [DOI: 10.1093/glycob/cwu065] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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De Paula VS, Pomin VH, Valente AP. Unique properties of human β-defensin 6 (hBD6) and glycosaminoglycan complex: sandwich-like dimerization and competition with the chemokine receptor 2 (CCR2) binding site. J Biol Chem 2014; 289:22969-22979. [PMID: 24970887 DOI: 10.1074/jbc.m114.572529] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Defensins are components of the innate immune system that promote the directional migration and activation of dendritic cells, thereby modulating the adaptive immune response. Because matrix glycosaminoglycan (GAG) is known to be important for these functions, we characterized the structural features of human β-defensin 6 (hBD6) and GAG interaction using a combination of structural and in silico analyses. Our results showed that GAG model compounds, a pentasaccharide (fondaparinux, FX) and an octasaccharide heparin derivative (dp8) bind to the α-helix and in the loops between the β2 and β3 strands, inducing the formation of a ternary complex with a 2:1 hBD6:FX stoichiometry. Competition experiments indicated an overlap of GAG and chemokine receptor CCR2 binding sites. An NMR-derived model of the ternary complex revealed that FX interacts with hBD6 along the dimerization interface, primarily contacting the α-helices and β2-β3 loops from each monomer. We further demonstrated that high-pressure NMR spectroscopy could capture an intermediate stage of hBD6-FX interaction, exhibiting features of a cooperative binding mechanism. Collectively, these data suggest a "sandwich-like" model in which two hBD6 molecules bind a single FX chain and provide novel structural insights into how defensin orchestrates leukocyte recruitment through GAG binding and G protein-coupled receptor activation. Despite the similarity to chemokines and hBD2, our data indicate different properties for the hBD6-GAG complex. This work adds significant information to the currently limited data available for the molecular structures and dynamics of defensin carbohydrate binding.
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Affiliation(s)
- Viviane S De Paula
- Centro Nacional de Ressonância Magnética Nuclear de Macromoléculas and Universidade Federal do Rio de Janeiro, Rio de Janeiro RJ 21941-902, Brazil; Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro RJ 21941-902, Brazil.
| | - Vitor H Pomin
- Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro RJ 21941-902, Brazil
| | - Ana Paula Valente
- Centro Nacional de Ressonância Magnética Nuclear de Macromoléculas and Universidade Federal do Rio de Janeiro, Rio de Janeiro RJ 21941-902, Brazil; Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro RJ 21941-902, Brazil.
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31
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Zulueta MML, Lin SY, Hu YP, Hung SC. Synthetic heparin and heparan sulfate oligosaccharides and their protein interactions. Curr Opin Chem Biol 2013; 17:1023-9. [DOI: 10.1016/j.cbpa.2013.10.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 10/01/2013] [Indexed: 11/28/2022]
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Peysselon F, Ricard-Blum S. Heparin-protein interactions: from affinity and kinetics to biological roles. Application to an interaction network regulating angiogenesis. Matrix Biol 2013; 35:73-81. [PMID: 24246365 DOI: 10.1016/j.matbio.2013.11.001] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2013] [Revised: 11/05/2013] [Accepted: 11/05/2013] [Indexed: 01/17/2023]
Abstract
Numerous extracellular proteins, growth factors, chemokines, cytokines, enzymes, lipoproteins, involved in a variety of biological processes, interact with heparin and/or heparan sulfate at the cell surface and in the extracellular matrix (ECM). The goal of this study is to investigate the relationship(s) between affinity and kinetics of heparin-protein interactions and the localization of the proteins, their intrinsic disorder and their biological roles. Most proteins bind to heparin with a higher affinity than their fragments and form more stable complexes with heparin than with heparan sulfate. Lipoproteins and matrisome-associated proteins (e.g. growth factors and cytokines) bind to heparin with very high affinity. Matrisome-associated proteins form transient complexes with heparin. However they bind to this glycosaminoglycan with a higher affinity than the proteins of the core matrisome, which contribute to ECM assembly and organization, and than the secreted proteins which are not associated with the ECM. The association rate of proteins with heparin is related to the intrinsic disorder of heparin-binding sites. Enzyme inhibitor activity, protein dimerization, skeletal system development and pathways in cancer are functionally associated with proteins displaying a high or very high affinity for heparin (KD<100 nM). Besides their use in investigating molecular recognition and functions, kinetics and affinity are essential to prioritize interactions in networks and to build network models as discussed for the interaction network established at the surface of endothelial cells by endostatin, a heparin-binding protein regulating angiogenesis.
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Affiliation(s)
- Franck Peysselon
- UMR 5086 CNRS, Université Lyon1, Institut de Biologie et Chimie des Protéines, 7 passage du Vercors, 69367 Lyon Cedex 07, France
| | - Sylvie Ricard-Blum
- UMR 5086 CNRS, Université Lyon1, Institut de Biologie et Chimie des Protéines, 7 passage du Vercors, 69367 Lyon Cedex 07, France.
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33
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Poluri KM, Joseph PRB, Sawant KV, Rajarathnam K. Molecular basis of glycosaminoglycan heparin binding to the chemokine CXCL1 dimer. J Biol Chem 2013; 288:25143-25153. [PMID: 23864653 DOI: 10.1074/jbc.m113.492579] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Glycosaminoglycan (GAG)-bound and soluble chemokine gradients in the vasculature and extracellular matrix mediate neutrophil recruitment to the site of microbial infection and sterile injury in the host tissue. However, the molecular principles by which chemokine-GAG interactions orchestrate these gradients are poorly understood. This, in part, can be directly attributed to the complex interrelationship between the chemokine monomer-dimer equilibrium and binding geometry and affinities that are also intimately linked to GAG length. To address some of this missing knowledge, we have characterized the structural basis of heparin binding to the murine CXCL1 dimer. CXCL1 is a neutrophil-activating chemokine and exists as both monomers and dimers (Kd = 36 μm). To avoid interference from monomer-GAG interactions, we designed a trapped dimer (dCXCL1) by introducing a disulfide bridge across the dimer interface. We characterized the binding of GAG heparin octasaccharide to dCXCL1 using solution NMR spectroscopy. Our studies show that octasaccharide binds orthogonally to the interhelical axis and spans the dimer interface and that heparin binding enhances the structural integrity of the C-terminal helical residues and stability of the dimer. We generated a quadruple mutant (H20A/K22A/K62A/K66A) on the basis of the binding data and observed that this mutant failed to bind heparin octasaccharide, validating our structural model. We propose that the stability enhancement of dimers upon GAG binding regulates in vivo neutrophil trafficking by increasing the lifetime of "active" chemokines, and that this structural knowledge could be exploited for designing inhibitors that disrupt chemokine-GAG interactions and neutrophil homing to the target tissue.
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Affiliation(s)
- Krishna Mohan Poluri
- From the Department of Biochemistry and Molecular Biology,; Sealy Center for Structural Biology and Molecular Biophysics, and
| | - Prem Raj B Joseph
- From the Department of Biochemistry and Molecular Biology,; Sealy Center for Structural Biology and Molecular Biophysics, and
| | - Kirti V Sawant
- From the Department of Biochemistry and Molecular Biology
| | - Krishna Rajarathnam
- From the Department of Biochemistry and Molecular Biology,; Sealy Center for Structural Biology and Molecular Biophysics, and; Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, Texas 77555.
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35
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Chemokine oligomerization in cell signaling and migration. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2013; 117:531-78. [PMID: 23663982 DOI: 10.1016/b978-0-12-386931-9.00020-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Chemokines are small proteins best known for their role in controlling the migration of diverse cells, particularly leukocytes. Upon binding to their G-protein-coupled receptors on the leukocytes, chemokines stimulate the signaling events that cause cytoskeletal rearrangements involved in cell movement, and migration of the cells along chemokine gradients. Depending on the cell type, chemokines also induce many other types of cellular responses including those related to defense mechanisms, cell proliferation, survival, and development. Historically, most research efforts have focused on the interaction of chemokines with their receptors, where monomeric forms of the ligands are the functionally relevant state. More recently, however, the importance of chemokine interactions with cell surface glycosaminoglycans has come to light, and in most cases appears to involve oligomeric chemokine structures. This review summarizes existing knowledge relating to the structure and function of chemokine oligomers, and emerging methodology for determining structures of complex chemokine assemblies in the future.
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36
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Nguyen LT, Vogel HJ. Structural perspectives on antimicrobial chemokines. Front Immunol 2012; 3:384. [PMID: 23293636 PMCID: PMC3531597 DOI: 10.3389/fimmu.2012.00384] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 11/30/2012] [Indexed: 12/14/2022] Open
Abstract
Chemokines are best known as signaling proteins in the immune system. Recently however, a large number of human chemokines have been shown to exert direct antimicrobial activity. This moonlighting activity appears to be related to the net high positive charge of these immune signaling proteins. Chemokines can be divided into distinct structural elements and some of these have been studied as isolated peptide fragments that can have their own antimicrobial activity. Such peptides often encompass the α-helical region found at the C-terminal end of the parent chemokines, which, similar to other antimicrobial peptides, adopt a well-defined membrane-bound amphipathic structure. Because of their relatively small size, intact chemokines can be studied effectively by NMR spectroscopy to examine their structures in solution. In addition, NMR relaxation experiments of intact chemokines can provide detailed information about the intrinsic dynamic behavior; such analyses have helped for example to understand the activity of TC-1, an antimicrobial variant of CXCL7/NAP-2. With chemokine dimerization and oligomerization influencing their functional properties, the use of NMR diffusion experiments can provide information about monomer-dimer equilibria in solution. Furthermore, NMR chemical shift perturbation experiments can be used to map out the interface between self-associating subunits. Moreover, the unusual case of XCL1/lymphotactin presents a chemokine that can interconvert between two distinct folds in solution, both of which have been elucidated. Finally, recent advances have allowed for the determination of the structures of chemokines in complex with glycosaminoglycans, a process that could interfere with their antimicrobial activity. Taken together, these studies highlight several different structural facets that contribute to the way in which chemokines exert their direct microbicidal actions.
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Affiliation(s)
- Leonard T Nguyen
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary Calgary, AB, Canada
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Ziarek JJ, Volkman BF. NMR in the Analysis of Functional Chemokine Interactions and Drug Discovery. DRUG DISCOVERY TODAY. TECHNOLOGIES 2012; 9:e227-314. [PMID: 23166561 DOI: 10.1016/j.ddtec.2012.04.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The involvement of chemokines and chemokine receptors in a great variety of pathological indications underscores their utility as therapeutic targets. In general, chemokine-mediated migration and signaling requires three distinct interactions: self-association, glycosaminoglycan (GAG) binding, and activation of G protein-coupled receptors (GPCRs). Solution-state nuclear magnetic resonance (NMR) spectroscopy has long been used to determine the apo structure of chemokines and monitor complex formation; however, it has never contributed directly to drug discovery efforts that are traditionally focused on the previously inaccessible chemokine receptors. Our lab recently demonstrated that NMR structures can be successfully utilized to direct drug discovery against chemokines. The ease of collecting chemokine structural data coupled with the increased efficiency of structure-based drug discovery campaigns makes chemokine-directed therapies particularly attractive. In addition, recent advances in sample preparation, spectrometer hardware, and pulse program development are allowing researchers to examine interactions with previously inaccessible partners - including full-length chemokine receptors. These developments will facilitate exploration of novel ways to modulate chemokine activity using structure-guided drug discovery.
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Affiliation(s)
- Joshua J Ziarek
- Department of Biochemistry, Medical College of Wisconsin, 8701 West Watertown Plank Road, Milwaukee, Wisconsin 53226 USA
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Ziarek JJ, Veldkamp CT, Zhang F, Murray NJ, Kartz GA, Liang X, Su J, Baker JE, Linhardt RJ, Volkman BF. Heparin oligosaccharides inhibit chemokine (CXC motif) ligand 12 (CXCL12) cardioprotection by binding orthogonal to the dimerization interface, promoting oligomerization, and competing with the chemokine (CXC motif) receptor 4 (CXCR4) N terminus. J Biol Chem 2012; 288:737-46. [PMID: 23148226 DOI: 10.1074/jbc.m112.394064] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The ability to interact with cell surface glycosaminoglycans (GAGs) is essential to the cell migration properties of chemokines, but association with soluble GAGs induces the oligomerization of most chemokines including CXCL12. Monomeric CXCL12, but not dimeric CXCL12, is cardioprotective in a number of experimental models of cardiac ischemia. We found that co-administration of heparin, a common treatment for myocardial infarction, abrogated the protective effect of CXCL12 in an ex vivo rat heart model for myocardial infarction. The interaction between CXCL12 and heparin oligosaccharides has previously been analyzed through mutagenesis, in vitro binding assays, and molecular modeling. However, complications from heparin-induced CXCL12 oligomerization and studies using very short oligosaccharides have led to inconsistent conclusions as to the residues involved, the orientation of the binding site, and whether it overlaps with the CXCR4 N-terminal site. We used a constitutively dimeric variant to simplify the NMR analysis of CXCL12-binding heparin oligosaccharides of varying length. Biophysical and mutagenic analyses reveal a CXCL12/heparin interaction surface that lies perpendicular to the dimer interface, does not involve the chemokine N terminus, and partially overlaps with the CXCR4-binding site. We further demonstrate that heparin-mediated enzymatic protection results from the promotion of dimerization rather than direct heparin binding to the CXCL12 N terminus. These results clarify the structural basis for GAG recognition by CXCL12 and lend insight into the development of CXCL12-based therapeutics.
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Affiliation(s)
- Joshua J Ziarek
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
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Muñoz-García JC, López-Prados J, Angulo J, Díaz-Contreras I, Reichardt N, de Paz JL, Martín-Lomas M, Nieto PM. Effect of the substituents of the neighboring ring in the conformational equilibrium of iduronate in heparin-like trisaccharides. Chemistry 2012; 18:16319-31. [PMID: 23143902 DOI: 10.1002/chem.201202770] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Indexed: 12/22/2022]
Abstract
Based on the structure of the regular heparin, we have prepared a smart library of heparin-like trisaccharides by incorporating some sulfate groups in the sequence α-D-GlcNS- (1-4)-α-L-Ido2S-(1-4)-α-D-GlcN. According to the 3D structure of heparin, which features one helix turn every four residues, this fragment corresponds to the minimum binding motif. We have performed a complete NMR study and found that the trisaccharides have a similar 3D structure to regular heparin itself, but their spectral properties are such that allow to extract very detailed information about distances and coupling constants as they are isotropic molecules. The characteristic conformational equilibrium of the central iduronate ring has been analyzed combining NMR and molecular dynamics and the populations of the conformers of the central iduronate ring have been calculated. We have found that in those compounds lacking the sulfate group at position 6 of the reducing end glucosamine, the population of (2)S(0) of the central iduronate residue is sensitive to the temperature decreasing to 19% at 278 K. On the contrary, the trisaccharides with 6-O-sulfate in the reducing end glucosamine keep the level of population constant with temperature circa 40% of (2)S(0) similar to that observed at room temperature. Another structural feature that has been revealed through this analysis is the larger flexibility of the L-IdoAS- D-GlcN glycosidic linkage, compared with the D-GlcNS-L-IdoA. We propose that this is the point where the heparin chain is bended to form structures far from the regular helix known as kink that have been proposed to play an important role in the specificity of the heparin-protein interaction.
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Affiliation(s)
- Juan Carlos Muñoz-García
- Glycosystems Laboratory, Instituto de Investigaciones Quimicas, CSIC-US, Americo Vespucio, 49, 41092 Sevilla, Spain
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Langeslay DJ, Beni S, Larive CK. A closer look at the nitrogen next door: 1H-15N NMR methods for glycosaminoglycan structural characterization. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2012; 216:169-174. [PMID: 22364674 DOI: 10.1016/j.jmr.2012.01.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Revised: 01/04/2012] [Accepted: 01/28/2012] [Indexed: 05/31/2023]
Abstract
Recently, experimental conditions were presented for the detection of the N-sulfoglucosamine (GlcNS) NHSO(3)(-) or sulfamate (1)H and (15)N NMR resonances of the pharmaceutically and biologically important glycosaminoglycan (GAG) heparin in aqueous solution. In the present work, we explore further the applicability of nitrogen-bound proton detection to provide structural information for GAGs. Compared to the detection of (15)N chemical shifts of aminosugars through long-range couplings using the IMPACT-HNMBC pulse sequence, the more sensitive two-dimensional (1)H-(15)N HSQC-TOCSY experiments provided additional structural data. The IMPACT-HNMBC experiment remains a powerful tool as demonstrated by the spectrum measured for the unsubstituted amine of 3-O-sulfoglucosamine (GlcN(3S)), which cannot be observed with the (1)H-(15)N HSQC-TOCSY experiment due to the fast exchange of the amino group protons with solvent. The (1)H-(15)N HSQC-TOCSY NMR spectrum reported for the mixture of model compounds GlcNS and N-acetylglucosamine (GlcNAc) demonstrate the broad utility of this approach. Measurements for the synthetic pentasaccharide drug Arixtra® (Fondaparinux sodium) in aqueous solution illustrate the power of this NMR pulse sequence for structural characterization of highly similar N-sulfoglucosamine residues in GAG-derived oligosaccharides.
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Affiliation(s)
- Derek J Langeslay
- Department of Chemistry, University of California-Riverside, Riverside, CA 92521, USA
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41
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Langeslay DJ, Beni S, Larive CK. Detection of the 1H and 15N NMR Resonances of Sulfamate Groups in Aqueous Solution: A New Tool for Heparin and Heparan Sulfate Characterization. Anal Chem 2011; 83:8006-10. [DOI: 10.1021/ac202144m] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Derek J. Langeslay
- Department of Chemistry, University of California−Riverside, Riverside, California 92521, United States
| | - Szabolcs Beni
- Department of Chemistry, University of California−Riverside, Riverside, California 92521, United States
- Semmelweis University, Department of Pharmaceutical Chemistry, Hőgyes Endre u. 9, H-1092 Budapest, Hungary
| | - Cynthia K. Larive
- Department of Chemistry, University of California−Riverside, Riverside, California 92521, United States
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