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Vessella G, Marchetti R, Del Prete A, Traboni S, Iadonisi A, Schiraldi C, Silipo A, Bedini E. Semisynthetic Isomers of Fucosylated Chondroitin Sulfate Polysaccharides with Fucosyl Branches at a Non-Natural Site. Biomacromolecules 2021; 22:5151-5161. [PMID: 34775751 PMCID: PMC8672353 DOI: 10.1021/acs.biomac.1c01112] [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] [Indexed: 11/29/2022]
Abstract
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The several interesting
activities detected for fucosylated chondroitin
sulfate (fCS) have fueled in the last years several efforts toward
the obtainment of fCS oligosaccharides and low molecular weight (LMW)
polysaccharides with a well-defined structure, in order to avoid the
problems associated with the potential employment of native, sea cucumber
sourced fCSs as a drug. Total synthesis and controlled depolymerization
of the natural fCS polysaccharides are the main approaches to this
aim; nonetheless, they present some limitations. These could be circumvented
by semisynthesis, a strategy relying upon the regioselective fucosylation
and sulfation of a microbial sourced polysaccharide sharing the same
chondroitin backbone of fCS but devoid of any fucose (Fuc) and sulfate
decoration on it. This approach is highly versatile, as it could open
access also to fCS isomers carrying Fuc and sulfate groups at non-natural
sites. Here we prepare for the first time some structurally homogeneous
fCS isomers through a multistep procedure with a glycosylation reaction
between a LMW polysaccharide acceptor and three different Fuc donors
as key step. The obtained products were subjected to a detailed structural
characterization by 2D-NMR. The conformational behavior was also investigated
by NMR and molecular dynamics simulation methods and compared with
data reported for natural fCS.
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Affiliation(s)
- Giulia Vessella
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario Monte S.Angelo, via Cintia 4, I-80126 Napoli, Italy
| | - Roberta Marchetti
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario Monte S.Angelo, via Cintia 4, I-80126 Napoli, Italy
| | - Angela Del Prete
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario Monte S.Angelo, via Cintia 4, I-80126 Napoli, Italy
| | - Serena Traboni
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario Monte S.Angelo, via Cintia 4, I-80126 Napoli, Italy
| | - Alfonso Iadonisi
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario Monte S.Angelo, via Cintia 4, I-80126 Napoli, Italy
| | - Chiara Schiraldi
- Department of Experimental Medicine, Section of Biotechnology, University of Campania "Luigi Vanvitelli", via de Crecchio 7, I-80138 Napoli, Italy
| | - Alba Silipo
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario Monte S.Angelo, via Cintia 4, I-80126 Napoli, Italy
| | - Emiliano Bedini
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario Monte S.Angelo, via Cintia 4, I-80126 Napoli, Italy
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2
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The Influences of Sulphation, Salt Type, and Salt Concentration on the Structural Heterogeneity of Glycosaminoglycans. Int J Mol Sci 2021; 22:ijms222111529. [PMID: 34768961 PMCID: PMC8583755 DOI: 10.3390/ijms222111529] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 10/12/2021] [Accepted: 10/14/2021] [Indexed: 12/15/2022] Open
Abstract
The increasing recognition of the biochemical importance of glycosaminoglycans (GAGs) has in recent times made them the center of attention of recent research investigations. It became evident that subtle conformational factors play an important role in determining the relationship between the chemical composition of GAGs and their activity. Therefore, a thorough understanding of their structural flexibility is needed, which is addressed in this work by means of all-atom molecular dynamics (MD) simulations. Four major GAGs with different substitution patterns, namely hyaluronic acid as unsulphated GAG, heparan-6-sulphate, chondroitin-4-sulphate, and chondroitin-6-sulphate, were investigated to elucidate the influence of sulphation on the dynamical features of GAGs. Moreover, the effects of increasing NaCl and KCl concentrations were studied as well. Different structural parameters were determined from the MD simulations, in combination with a presentation of the free energy landscape of the GAG conformations, which allowed us to unravel the conformational fingerprints unique to each GAG. The largest effects on the GAG structures were found for sulphation at position 6, as well as binding of the metal ions in the absence of chloride ions to the carboxylate and sulphate groups, which both increase the GAG conformational flexibility.
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3
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Lu J, Zhou F, Liu W, Yu F. Mass spectrometry assisted arginine side chains assignment of NMR resonances in natural abundance proteins. JOURNAL OF BIOMOLECULAR NMR 2020; 74:173-181. [PMID: 32008172 DOI: 10.1007/s10858-020-00302-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 01/27/2020] [Indexed: 06/10/2023]
Abstract
Arginine side chains play critical roles in many protein-ligand interactions and enzyme catalysis. Unambiguous resonance assignment is a prerequisite for the nuclear magnetic resonance (NMR) spectroscopy studies of arginine side chains dynamics and hydrogen exchange properties from which one can expect to elucidate in more detail the roles of arginine residues in protein structure and function. Here we present a new mass spectrometry (MS)-based method for assigning the side-chain resonances of arginine residues in 2D 1H-15N NMR spectra. The method requires no additional isotopic labeling, and relies on knowledge of the amino acid sequence, the modification of the guanidino groups and liquid chromatography-mass spectrometry rather than the protein's structure or properties. Correlating the modification rates can connect cross-peak positions from NMR data with MS data to support resonances assignments. In the present work, we have extended our original application to natural abundance human ubiquitin to provide ε-NH assessments of three arginine for this well-studied protein.
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Affiliation(s)
- Jingjing Lu
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, China
- State Key Laboratory of Long-Acting and Targeting Drug Delivery Technologies, Shandong Luye Pharmaceutical Co. Ltd., Yantai, China
| | - Fengmei Zhou
- State Key Laboratory of Long-Acting and Targeting Drug Delivery Technologies, Shandong Luye Pharmaceutical Co. Ltd., Yantai, China
| | - Wanhui Liu
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, China
| | - Fei Yu
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, China.
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4
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Nagarajan B, Sankaranarayanan NV, Desai UR. Perspective on computational simulations of glycosaminoglycans. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2019; 9:e1388. [PMID: 31080520 PMCID: PMC6504973 DOI: 10.1002/wcms.1388] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 07/07/2018] [Indexed: 01/06/2023]
Abstract
Glycosaminoglycans (GAGs) represent a formidable frontier for chemists, biochemists, biologists, medicinal chemists and drug delivery specialists because of massive structural complexity. GAGs are arguably the most complex, natural linear biopolymers with theoretical diversity orders of magnitude higher than proteins and nucleic acids. Yet, this diversity remains generally untapped. Computational approaches offer major routes to understand GAG structure and dynamics so as to enable novel applications of these biopolymers. In fact, computational algorithms, softwares, online tools and techniques have reached a level of sophistication that help understand atomistic details of conformational variation and protein recognition of individual GAG sequences. This review describes current approaches and challenges in computational study of GAGs. It presents a history of major findings since the earliest mention of GAGs (the 1960s), the development of parameters and force fields specific for GAGs, and the application of these tools in understanding GAG structure-function relationship. This review also presents a section on how to perform simulation of GAGs, which is directed toward researchers interested in entering this promising field with potential to impact therapy.
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Affiliation(s)
- Balaji Nagarajan
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond,
VA 23298, USA
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Nehru Viji Sankaranarayanan
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond,
VA 23298, USA
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Umesh R. Desai
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond,
VA 23298, USA
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA
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5
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Profant V, Johannessen C, Blanch EW, Bouř P, Baumruk V. Effects of sulfation and the environment on the structure of chondroitin sulfate studied via Raman optical activity. Phys Chem Chem Phys 2019; 21:7367-7377. [DOI: 10.1039/c9cp00472f] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Raman optical activity reflects differences in the secondary structure of chondroitin caused by its sulfation.
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Affiliation(s)
- Václav Profant
- Institute of Physics
- Faculty of Mathematics and Physics
- Charles University
- 121 16 Prague 2
- Czech Republic
| | | | | | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences
- 166 10 Prague 6
- Czech Republic
| | - Vladimír Baumruk
- Institute of Physics
- Faculty of Mathematics and Physics
- Charles University
- 121 16 Prague 2
- Czech Republic
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6
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de Souza JF, Lessa EF, Nörnberg A, Gularte MS, Quadrado RF, Fajardo AR. Enzymatic depolymerization – An easy approach to reduce the chondroitin sulfate molecular weight. Process Biochem 2018. [DOI: 10.1016/j.procbio.2018.08.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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7
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Yin R, Zhou L, Gao N, Li Z, Zhao L, Shang F, Wu M, Zhao J. Oligosaccharides from depolymerized fucosylated glycosaminoglycan: Structures and minimum size for intrinsic factor Xase complex inhibition. J Biol Chem 2018; 293:14089-14099. [PMID: 30030375 PMCID: PMC6130965 DOI: 10.1074/jbc.ra118.003809] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 07/13/2018] [Indexed: 01/01/2023] Open
Abstract
Fucosylated glycosaminoglycan (FG), a structurally complex glycosaminoglycan found up to now exclusively in sea cucumbers, has distinct anticoagulant properties, notably a strong inhibitory activity of intrinsic factor Xase complex (FXase). Knowledge of the FG structures could facilitate the development of a clinically effective intrinsic FXase inhibitor for anticoagulant drugs. Here, a new fucosylated glycosaminoglycan was obtained from the widely traded sea cucumber Bohadschia argus The precise structure was deduced as {→4)-[l-Fuc3S4S-α-(1→3)-]-d-GlcA-β-(1→3)-d-GalNAc4S6S-β-(1} through analysis of its chemical properties and homogeneous oligosaccharides purified from its β-eliminative depolymerized products. The B. argus FG with mostly 3,4-di-O-sulfated fucoses expands our knowledge on FG structural types. This β-elimination process, producing oligosaccharides with well-defined structures, is a powerful tool for analyzing the structure of complex FGs. Among these oligosaccharides, an octasaccharide displayed potent FXase inhibitory activity. Compared with oligosaccharides with various degrees of polymerization (3n and 3n - 1), our analyses reveal that the purified octasaccharide is the minimum structural unit responsible for the potent selective FXase inhibition, because the d-talitol in the nonsaccharide is unnecessary. The octasaccharide with 2,4-di-O-sulfated fucoses is more potent than that of one with 3,4-di-O-sulfated fucoses. Thus, sulfation patterns can play an important role in the inhibition of intrinsic factor Xase complex.
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Affiliation(s)
- Ronghua Yin
- From the State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China and
- the University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lutan Zhou
- From the State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China and
- the University of Chinese Academy of Sciences, Beijing 100049, China
| | - Na Gao
- From the State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China and
| | - Zi Li
- From the State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China and
| | - Longyan Zhao
- From the State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China and
| | - Feineng Shang
- From the State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China and
| | - Mingyi Wu
- From the State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China and
| | - Jinhua Zhao
- From the State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China and
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8
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Abstract
Complex carbohydrates are ubiquitous in nature, and together with proteins and nucleic acids they comprise the building blocks of life. But unlike proteins and nucleic acids, carbohydrates form nonlinear polymers, and they are not characterized by robust secondary or tertiary structures but rather by distributions of well-defined conformational states. Their molecular flexibility means that oligosaccharides are often refractory to crystallization, and nuclear magnetic resonance (NMR) spectroscopy augmented by molecular dynamics (MD) simulation is the leading method for their characterization in solution. The biological importance of carbohydrate-protein interactions, in organismal development as well as in disease, places urgency on the creation of innovative experimental and theoretical methods that can predict the specificity of such interactions and quantify their strengths. Additionally, the emerging realization that protein glycosylation impacts protein function and immunogenicity places the ability to define the mechanisms by which glycosylation impacts these features at the forefront of carbohydrate modeling. This review will discuss the relevant theoretical approaches to studying the three-dimensional structures of this fascinating class of molecules and interactions, with reference to the relevant experimental data and techniques that are key for validation of the theoretical predictions.
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Affiliation(s)
- Robert J Woods
- Complex Carbohydrate Research Center and Department of Biochemistry and Molecular Biology , University of Georgia , 315 Riverbend Road , Athens , Georgia 30602 , United States
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9
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Yu F, Qiao J, Robblee J, Tsao D, Anderson J, Capila I. An Integrated Approach to Unique NMR Assignment of Methionine Methyl Resonances in Proteins. Anal Chem 2017; 89:1610-1616. [PMID: 28208280 DOI: 10.1021/acs.analchem.6b03705] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Fei Yu
- Momenta Pharmaceuticals Inc., 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Jing Qiao
- Momenta Pharmaceuticals Inc., 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - John Robblee
- Momenta Pharmaceuticals Inc., 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Desiree Tsao
- Momenta Pharmaceuticals Inc., 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - James Anderson
- Momenta Pharmaceuticals Inc., 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Ishan Capila
- Momenta Pharmaceuticals Inc., 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
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10
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Soares PA, Queiroz IN, Pomin VH. NMR structural biology of sulfated glycans. J Biomol Struct Dyn 2016; 35:1069-1084. [DOI: 10.1080/07391102.2016.1171165] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Paulo A.G. Soares
- 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
| | - Ismael N.L. Queiroz
- 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
| | - Vitor H. Pomin
- Program of Glycobiology, Institute of Medical Biochemistry Leopoldo de Meis, and University Hospital Clementino Fraga Filho, Federal University of Rio de Janeiro , Rio de Janeiro, RJ 21941-913, Brazil
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11
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Interactions of the Chemokine CCL5/RANTES with Medium-Sized Chondroitin Sulfate Ligands. Structure 2015; 23:1066-77. [PMID: 25982530 DOI: 10.1016/j.str.2015.03.024] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 03/23/2015] [Accepted: 03/31/2015] [Indexed: 12/22/2022]
Abstract
Interactions of the chemokine CCL5 (RANTES) with glycosaminoglycans (GAGs) are crucial to the CCL5-mediated inflammation process. However, structural information on interactions between CCL5 and longer GAG fragments is lacking. In this study, the interactions between oligosaccharides derived from chondroitin sulfate and a dimeric variant of CCL5 were investigated using solution nuclear magnetic resonance. The data indicate that, in addition to the BBXB motif in the 40s loop, GAGs also contact residues in the N loop in a manner similar to interactions between chemokine and the receptor N terminus, leading to possible stabilization of the dimer. Using 2,2,6,6-tetramethylpiperidin-1-yl)oxidanyl-tagged hexasaccharides, the binding orientation of the hexasaccharides was shown to be highly dependent on the sulfation pattern of the N-acetyl galactosamine groups. Finally, a model of the CCL5 dimer complexed to chondroitin sulfate hexasaccharides was constructed using paramagnetic relaxation enhancement and intra- and intermolecular nuclear Overhauser effect constraints.
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12
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Faller CE, Guvench O. Sulfation and cation effects on the conformational properties of the glycan backbone of chondroitin sulfate disaccharides. J Phys Chem B 2015; 119:6063-73. [PMID: 25906376 DOI: 10.1021/jp511431q] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Chondroitin sulfate (CS) is one of several glycosaminoglycans that are major components of proteoglycans. A linear polymer consisting of repeats of the disaccharide -4GlcAβ1-3GalNAcβ1-, CS undergoes differential sulfation resulting in five unique sulfation patterns. Because of the dimer repeat, the CS glycosidic "backbone" has two distinct sets of conformational degrees of freedom defined by pairs of dihedral angles: (ϕ1, ψ1) about the β1-3 glycosidic linkage and (ϕ2, ψ2) about the β1-4 glycosidic linkage. Differential sulfation and the possibility of cation binding, combined with the conformational flexibility and biological diversity of CS, complicate experimental efforts to understand CS three-dimensional structures at atomic resolution. Therefore, all-atom explicit-solvent molecular dynamics simulations with Adaptive Biasing Force sampling of the CS backbone were applied to obtain high-resolution, high-precision free energies of CS disaccharides as a function of all possible backbone geometries. All 10 disaccharides (β1-3 vs β1-4 linkage × five different sulfation patterns) were studied; additionally, ion effects were investigated by considering each disaccharide in the presence of either neutralizing sodium or calcium cations. GlcAβ1-3GalNAc disaccharides have a single, broad, thermodynamically important free-energy minimum, whereas GalNAcβ1-4GlcA disaccharides have two such minima. Calcium cations but not sodium cations bind to the disaccharides, and binding is primarily to the GlcA -COO(-) moiety as opposed to sulfate groups. This binding alters the glycan backbone thermodynamics in instances where a calcium cation bound to -COO(-) can act to bridge and stabilize an interaction with an adjacent sulfate group, whereas, in the absence of this cation, the proximity of a sulfate group to -COO(-) results in two like charges being both desolvated and placed adjacent to each other and is found to be destabilizing. In addition to providing information on sulfation and cation effects, the present results can be applied to building models of CS polymers and as a point of comparison in studies of CS polymer backbone dynamics and thermodynamics.
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Affiliation(s)
- Christina E Faller
- Department of Pharmaceutical Sciences, University of New England College of Pharmacy, 716 Stevens Avenue, Portland, Maine 04103, United States
| | - Olgun Guvench
- Department of Pharmaceutical Sciences, University of New England College of Pharmacy, 716 Stevens Avenue, Portland, Maine 04103, United States
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Panagos CG, Thomson DS, Moss C, Hughes AD, Kelly MS, Liu Y, Chai W, Venkatasamy R, Spina D, Page CP, Hogwood J, Woods RJ, Mulloy B, Bavington CD, Uhrín D. Fucosylated chondroitin sulfates from the body wall of the sea cucumber Holothuria forskali: conformation, selectin binding, and biological activity. J Biol Chem 2014; 289:28284-98. [PMID: 25147180 PMCID: PMC4192483 DOI: 10.1074/jbc.m114.572297] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 08/09/2014] [Indexed: 11/06/2022] Open
Abstract
Fucosylated chondroitin sulfate (fCS) extracted from the sea cucumber Holothuria forskali is composed of the following repeating trisaccharide unit: → 3)GalNAcβ4,6S(1 → 4) [FucαX(1 → 3)]GlcAβ(1 →, where X stands for different sulfation patterns of fucose (X = 3,4S (46%), 2,4S (39%), and 4S (15%)). As revealed by NMR and molecular dynamics simulations, the fCS repeating unit adopts a conformation similar to that of the Le(x) blood group determinant, bringing several sulfate groups into close proximity and creating large negative patches distributed along the helical skeleton of the CS backbone. This may explain the high affinity of fCS oligosaccharides for L- and P-selectins as determined by microarray binding of fCS oligosaccharides prepared by Cu(2+)-catalyzed Fenton-type and photochemical depolymerization. No binding to E-selectin was observed. fCS poly- and oligosaccharides display low cytotoxicity in vitro, inhibit human neutrophil elastase activity, and inhibit the migration of neutrophils through an endothelial cell layer in vitro. Although the polysaccharide showed some anti-coagulant activity, small oligosaccharide fCS fragments had much reduced anticoagulant properties, with activity mainly via heparin cofactor II. The fCS polysaccharides showed prekallikrein activation comparable with dextran sulfate, whereas the fCS oligosaccharides caused almost no effect. The H. forskali fCS oligosaccharides were also tested in a mouse peritoneal inflammation model, where they caused a reduction in neutrophil infiltration. Overall, the data presented support the action of fCS as an inhibitor of selectin interactions, which play vital roles in inflammation and metastasis progression. Future studies of fCS-selectin interaction using fCS fragments or their mimetics may open new avenues for therapeutic intervention.
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Affiliation(s)
- Charalampos G Panagos
- From the EaStCHEM School of Chemistry, Joseph Black Building, The King's Buildings, University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom
| | - Derek S Thomson
- GlycoMar Ltd., European Centre for Marine Biotechnology, Dunstaffnage Marine Laboratory, Oban, Argyll PA37 1QA, United Kingdom
| | - Claire Moss
- GlycoMar Ltd., European Centre for Marine Biotechnology, Dunstaffnage Marine Laboratory, Oban, Argyll PA37 1QA, United Kingdom
| | - Adam D Hughes
- the Scottish Association for Marine Science, Scottish Marine Institute, Oban, Argyll PA37 1QA, United Kingdom
| | - Maeve S Kelly
- the Scottish Association for Marine Science, Scottish Marine Institute, Oban, Argyll PA37 1QA, United Kingdom
| | - Yan Liu
- the Glycosciences Laboratory, Hammersmith Campus, Imperial College London, London W12 0NN, United Kingdom
| | - Wengang Chai
- the Glycosciences Laboratory, Hammersmith Campus, Imperial College London, London W12 0NN, United Kingdom
| | - Radhakrishnan Venkatasamy
- the Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London SE1 9NH, United Kingdom
| | - Domenico Spina
- the Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London SE1 9NH, United Kingdom
| | - Clive P Page
- the Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London SE1 9NH, United Kingdom
| | - John Hogwood
- the National Institute of Biological Standards and Controls, South Mimms, Potters Bar, Hertfordshire EN6 3QG, United Kingdom
| | - Robert J Woods
- the Complex Carbohydrate Research Center, the University of Georgia, Athens, Georgia 30602, and the School of Chemistry, National University of Ireland Galway, University Road, Galway, Ireland
| | - Barbara Mulloy
- the Glycosciences Laboratory, Hammersmith Campus, Imperial College London, London W12 0NN, United Kingdom, the Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London SE1 9NH, United Kingdom
| | - Charlie D Bavington
- GlycoMar Ltd., European Centre for Marine Biotechnology, Dunstaffnage Marine Laboratory, Oban, Argyll PA37 1QA, United Kingdom
| | - Dušan Uhrín
- From the EaStCHEM School of Chemistry, Joseph Black Building, The King's Buildings, University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom,
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14
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Fajardo AR, Guerry A, Britta EA, Nakamura CV, Muniz EC, Borsali R, Halila S. Sulfated glycosaminoglycan-based block copolymer: preparation of biocompatible chondroitin sulfate-b-poly(lactic acid) micelles. Biomacromolecules 2014; 15:2691-700. [PMID: 24857763 DOI: 10.1021/bm5005355] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Despite a growing interest in amphiphilic polysaccharide-based diblock copolymers as functional polymeric drug delivery nanosystems, biologically relevant sulfated glycosaminoglycan systems were not yet investigated. Here, we report the synthesis and the self-assembly properties in water of chondroitin sulfate-b-poly(lactic acid) (CS-b-PLA(n)). The CS-b-PLA(n) were synthesized using click-grafting onto method implying reducing-end alkynation of low-molecular weight depolymerized CS (M(w) = 5000 g·mol(-1)) and azide-terminated functionalization of PLAn (M(w) = 6500 g·mol(-1) (n = 46) and M(w) = 1700 g·mol(-1) (n = 20)). The diblock copolymer self-assembled in water giving rise to spherical micelles that were characterized in solution using dynamic/static light scattering and at dry state by TEM technique. In vitro assays on healthy cells showed that at high concentrations, up to 10 μg·mL(-1), CS-b-PLA(n) were noncytotoxic. Those preliminary studies are promising in the perspective to use them as biocompatible nanovehicles for anticancer drug delivery.
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Affiliation(s)
- André R Fajardo
- Centre de Recherches sur les Macromolécules Végétales (CERMAV, UPR-CNRS 5301), Université Grenoble Alpes , BP 53, 38041 Grenoble Cedex 9, France
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Miller T, Goude MC, McDevitt TC, Temenoff JS. Molecular engineering of glycosaminoglycan chemistry for biomolecule delivery. Acta Biomater 2014; 10:1705-19. [PMID: 24121191 PMCID: PMC3960340 DOI: 10.1016/j.actbio.2013.09.039] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Revised: 09/19/2013] [Accepted: 09/30/2013] [Indexed: 12/22/2022]
Abstract
Glycosaminoglycans (GAGs) are linear, negatively charged polysaccharides that interact with a variety of positively charged growth factors. In this review article the effects of engineering GAG chemistry for molecular delivery applications in regenerative medicine are presented. Three major areas of focus at the structure-function-property interface are discussed: (1) macromolecular properties of GAGs; (2) effects of chemical modifications on protein binding; (3) degradation mechanisms of GAGs. GAG-protein interactions can be based on: (1) GAG sulfation pattern; (2) GAG carbohydrate conformation; (3) GAG polyelectrolyte behavior. Chemical modifications of GAGs, which are commonly performed to engineer molecular delivery systems, affect protein binding and are highly dependent on the site of modification on the GAG molecules. The rate and mode of degradation can determine the release of molecules as well as the length of GAG fragments to which the cargo is electrostatically coupled and eventually released from the delivery system. Overall, GAG-based polymers are a versatile biomaterial platform offering novel means to engineer molecular delivery systems with a high degree of control in order to better treat a range of degenerated or injured tissues.
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Affiliation(s)
- Tobias Miller
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive, Atlanta, GA 30332, USA
| | - Melissa C Goude
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive, Atlanta, GA 30332, USA
| | - Todd C McDevitt
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive, Atlanta, GA 30332, USA; Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Johnna S Temenoff
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive, Atlanta, GA 30332, USA; Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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16
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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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17
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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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18
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Lundborg M, Fontana C, Widmalm G. Automatic structure determination of regular polysaccharides based solely on NMR spectroscopy. Biomacromolecules 2011; 12:3851-5. [PMID: 21955217 PMCID: PMC3215282 DOI: 10.1021/bm201169y] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2011] [Revised: 09/20/2011] [Indexed: 01/22/2023]
Abstract
The structural analysis of polysaccharides requires that the sugar components and their absolute configurations are determined. We here show that this can be performed based on NMR spectroscopy by utilizing butanolysis with (+)- and (-)-2-butanol that gives the corresponding 2-butyl glycosides with characteristic (1)H and (13)C NMR chemical shifts. The subsequent computer-assisted structural determination by CASPER can then be based solely on NMR data in a fully automatic way as shown and implemented herein. The method is additionally advantageous in that reference data only have to be prepared once and from a user's point of view only the unknown sample has to be derivatized for use in CASPER.
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Affiliation(s)
- Magnus Lundborg
- Department of Organic Chemistry,
Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - Carolina Fontana
- Department of Organic Chemistry,
Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - Göran Widmalm
- Department of Organic Chemistry,
Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
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19
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Roldós V, Cañada FJ, Jiménez-Barbero J. Carbohydrate-Protein Interactions: A 3D View by NMR. Chembiochem 2011; 12:990-1005. [DOI: 10.1002/cbic.201000705] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2010] [Indexed: 12/29/2022]
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20
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Wang X, Lee HW, Liu Y, Prestegard JH. Structural NMR of protein oligomers using hybrid methods. J Struct Biol 2011; 173:515-29. [PMID: 21074622 PMCID: PMC3040251 DOI: 10.1016/j.jsb.2010.11.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Revised: 10/03/2010] [Accepted: 11/04/2010] [Indexed: 11/19/2022]
Abstract
Solving structures of native oligomeric protein complexes using traditional high-resolution NMR techniques remains challenging. However, increased utilization of computational platforms, and integration of information from less traditional NMR techniques with data from other complementary biophysical methods, promises to extend the boundary of NMR-applicable targets. This article reviews several of the techniques capable of providing less traditional and complementary structural information. In particular, the use of orientational constraints coming from residual dipolar couplings and residual chemical shift anisotropy offsets are shown to simplify the construction of models for oligomeric complexes, especially in cases of weak homo-dimers. Combining this orientational information with interaction site information supplied by computation, chemical shift perturbation, paramagnetic surface perturbation, cross-saturation and mass spectrometry allows high resolution models of the complexes to be constructed with relative ease. Non-NMR techniques, such as mass spectrometry, EPR and small angle X-ray scattering, are also expected to play increasingly important roles by offering alternative methods of probing the overall shape of the complex. Computational platforms capable of integrating information from multiple sources in the modeling process are also discussed in the article. And finally a new, detailed example on the determination of a chemokine tetramer structure will be used to illustrate how a non-traditional approach to oligomeric structure determination works in practice.
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Affiliation(s)
- Xu Wang
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602. USA
| | - Hsiau-Wei Lee
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602. USA
| | - Yizhou Liu
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602. USA
| | - James H. Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602. USA
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21
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Pomin VH, Sharp JS, Li X, Wang L, Prestegard JH. Characterization of glycosaminoglycans by 15N NMR spectroscopy and in vivo isotopic labeling. Anal Chem 2010; 82:4078-88. [PMID: 20423049 DOI: 10.1021/ac1001383] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Characterization of glycosaminoglycans (GAGs), including chondroitin sulfate (CS), dermatan sulfate (DS), and heparan sulfate (HS), is important in developing an understanding of cellular function and in assuring quality of preparations destined for biomedical applications. While use of (1)H and (13)C NMR spectroscopy has become common in characterization of these materials, spectra are complex and difficult to interpret when a more heterogeneous GAG type or a mixture of several types is present. Herein a method based on (1)H-(15)N two-dimensional NMR experiments is described. The (15)N- and (1)H-chemical shifts of amide signals from (15)N-containing acetylgalactosamines in CSs are shown to be quite sensitive to the sites of sulfation (4-, 6-, or 4,6-) and easily distinguishable from those of DS. The amide signals from residual (15)N-containing acetylglucosamines in HS are shown to be diagnostic of the presence of these GAG components as well. Most data were collected at natural abundance of (15)N despite its low percentage. However enrichment of the (15)N-content in GAGs using metabolic incorporation from (15)N-glutamine added to cell culture media is also demonstrated and used to distinguish metabolic states in different cell types.
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Affiliation(s)
- Vitor H Pomin
- Complex Carbohydrate Research Center, 315 Riverbend Road, University of Georgia, Athens, Georgia 30602, USA
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22
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Liu Y, Prestegard JH. A device for the measurement of residual chemical shift anisotropy and residual dipolar coupling in soluble and membrane-associated proteins. JOURNAL OF BIOMOLECULAR NMR 2010; 47:249-58. [PMID: 20506033 PMCID: PMC2941885 DOI: 10.1007/s10858-010-9427-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2010] [Accepted: 05/12/2010] [Indexed: 05/13/2023]
Abstract
Residual dipolar coupling (RDC) and residual chemical shift anisotropy (RCSA) report on orientational properties of a dipolar bond vector and a chemical shift anisotropy principal axis system, respectively. They can be highly complementary in the analysis of backbone structure and dynamics in proteins as RCSAs generally include a report on vectors out of a peptide plane while RDCs usually report on in-plane vectors. Both RDC and RCSA average to zero in isotropic solutions and require partial orientation in a magnetic field to become observable. While the alignment and measurement of RDC has become routine, that of RCSA is less common. This is partly due to difficulties in providing a suitable isotopic reference spectrum for the measurement of the small chemical shift offsets coming from RCSA. Here we introduce a device (modified NMR tube) specifically designed for accurate measurement of reference and aligned spectra for RCSA measurements, but with a capacity for RDC measurements as well. Applications to both soluble and membrane anchored proteins are illustrated.
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23
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Cilpa G, Hyvönen MT, Koivuniemi A, Riekkola ML. Atomistic insight into chondroitin-6-sulfate glycosaminoglycan chain through quantum mechanics calculations and molecular dynamics simulation. J Comput Chem 2010; 31:1670-80. [PMID: 20087899 DOI: 10.1002/jcc.21453] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Chondroitin-6-sulfate (C6S) is a glycosaminoglycan (GAG) constituent in the extracellular matrix, which participates actively in crucial biological processes, as well as in various pathological conditions, such as atherosclerosis and cancer. Molecular interactions involving the C6S chain are therefore of considerable interest. A computational model for atomistic simulation was built. This work describes the design and validation of a force field for a C6S dodecasaccharide chain. The results of an extensive molecular dynamics simulation performed with the new force field provide a novel insight into the structure and dynamics of the C6S chain. The intramolecular H-bonds in the disaccharide linkage region are suggested to play a major role in determining the chain structural dynamics. Moreover, the unravelling of an additional H-bond involving the sulfate groups in C6S is interesting as changes in sulfation have been claimed to be an important factor in several diseases. The force field will prove useful for future studies of crucial interactions between C6S and various nanoassemblies. It can also be used as a basis for modeling of other GAGs.
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Affiliation(s)
- G Cilpa
- Laboratory of Analytical Chemistry, Department of Chemistry, University of Helsinki, P.O. Box 55, FI-00014 Helsinki, Finland.
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24
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Less is more when simulating unsulfated glycosaminoglycan 3D-structure: Comparison of GLYCAM06/TIP3P, PM3-CARB1/TIP3P, and SCC-DFTB-D/TIP3P predictions with experiment. J Comput Chem 2010; 31:2932-47. [DOI: 10.1002/jcc.21589] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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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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Abstract
More than half of all human proteins are glycosylated. Glycosylation defines the adhesive properties of glycoconjugates and it is largely through glycan-protein interactions that cell-cell and cell-pathogen contacts occur. Not surprisingly, considering the central role they play in molecular encounters, glycoprotein and carbohydrate-based drugs and therapeutics represent a greater than $20 billion market. Glycomics, the study of glycan expression in biological systems, relies on effective analytical techniques for correlation of glycan structure with function. This overview summarizes techniques developed historically for glycan characterization as well as recent trends. Derivatization methods key to both traditional and modern approaches for glycoanalysis are described. Monosaccharide compositional analysis is fundamental to any effort to understand glycan structure-function relationships. Chromatographic and electrophoretic separations are key parts of any glycoanalytical workflow. Mass spectrometry and nuclear magnetic resonance are complementary instrumental techniques for glycan analysis. Finally, microarrays are emerging as powerful new tools for dynamic analysis of glycan expression.
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Affiliation(s)
- Alicia M Bielik
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
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27
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Sattelle BM, Shakeri J, Roberts IS, Almond A. A 3D-structural model of unsulfated chondroitin from high-field NMR: 4-sulfation has little effect on backbone conformation. Carbohydr Res 2009; 345:291-302. [PMID: 20022001 PMCID: PMC3098369 DOI: 10.1016/j.carres.2009.11.013] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2009] [Revised: 11/06/2009] [Accepted: 11/10/2009] [Indexed: 11/26/2022]
Abstract
The glycosaminoglycan chondroitin sulfate is essential in human health and disease but exactly how sulfation dictates its 3D-structure at the atomic level is unclear. To address this, we have purified homogenous oligosaccharides of unsulfated chondroitin (with and without (15)N-enrichment) and analysed them by high-field NMR to make a comparison published chondroitin sulfate and hyaluronan 3D-structures. The result is the first full assignment of the tetrasaccharide and an experimental 3D-model of the hexasaccharide (PDB code 2KQO). In common with hyaluronan, we confirm that the amide proton is not involved in strong, persistent inter-residue hydrogen bonds. However, in contrast to hyaluronan, a hydrogen bond is not inferred between the hexosamine OH-4 and the glucuronic acid O5 atoms across the beta(1-->3) glycosidic linkage. The unsulfated chondroitin bond geometry differs slightly from hyaluronan by rotation about the beta(1-->3) psi dihedral (as previously predicted by simulation), while the beta(1-->4) linkage is unaffected. Furthermore, comparison shows that this glycosidic linkage geometry is similar in chondroitin-4-sulfate. We therefore hypothesise that both hexosamine OH-4 and OH-6 atoms are solvent exposed in chondroitin, explaining why it is amenable to sulfation and hyaluronan is not, and also that 4-sulfation has little effect on backbone conformation. Our conclusions exemplify the value of the 3D-model presented here and progress our understanding of glycosaminoglycan molecular properties.
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Affiliation(s)
- Benedict M Sattelle
- Manchester Interdisciplinary Biocentre, 131 Princess Street, Manchester, M1 7DN, UK
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28
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Slynko V, Schubert M, Numao S, Kowarik M, Aebi M, Allain FHT. NMR Structure Determination of a Segmentally Labeled Glycoprotein Using in Vitro Glycosylation. J Am Chem Soc 2009; 131:1274-81. [DOI: 10.1021/ja808682v] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Vadim Slynko
- Institute of Molecular Biology and Biophysics, and Institute of Microbiology, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Mario Schubert
- Institute of Molecular Biology and Biophysics, and Institute of Microbiology, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Shin Numao
- Institute of Molecular Biology and Biophysics, and Institute of Microbiology, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Michael Kowarik
- Institute of Molecular Biology and Biophysics, and Institute of Microbiology, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Markus Aebi
- Institute of Molecular Biology and Biophysics, and Institute of Microbiology, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Frédéric H.-T. Allain
- Institute of Molecular Biology and Biophysics, and Institute of Microbiology, ETH Zürich, CH-8093 Zürich, Switzerland
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29
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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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30
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Abstract
Oligo- and polysaccharides are infamous for being extremely flexible molecules, populating a series of well-defined rotational isomeric states under physiological conditions. Characterization of this heterogeneous conformational ensemble has been a major obstacle impeding high-resolution structure determination of carbohydrates and acting as a bottleneck in the effort to understand the relationship between the carbohydrate structure and function. This challenge has compelled the field to develop and apply theoretical and experimental methods that can explore conformational ensembles by both capturing and deconvoluting the structural and dynamic properties of carbohydrates. This review focuses on computational approaches that have been successfully used in combination with experiment to detail the three-dimensional structure of carbohydrates in a solution and in a complex with proteins. In addition, emerging experimental techniques for three-dimensional structural characterization of carbohydrate-protein complexes and future challenges in the field of structural glycobiology are discussed. The review is divided into five sections: (1) The complexity and plasticity of carbohydrates, (2) Predicting carbohydrate-protein interactions, (3) Calculating relative and absolute binding free energies for carbohydrate-protein complexes, (4) Emerging and evolving techniques for experimental characterization of carbohydrate-protein structures, and (5) Current challenges in structural glycoscience.
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Affiliation(s)
- Mari L DeMarco
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602-4712, USA
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602-4712, USA
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31
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Gemma E, Meyer O, Uhrín D, Hulme AN. Enabling methodology for the end functionalisation of glycosaminoglycan oligosaccharides. MOLECULAR BIOSYSTEMS 2008; 4:481-95. [DOI: 10.1039/b801666f] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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