1
|
Balogh G, Gyöngyösi T, Timári I, Herczeg M, Borbás A, Sadiq SK, Fehér K, Kövér KE. Conformational Analysis of Heparin-Analogue Pentasaccharides by Nuclear Magnetic Resonance Spectroscopy and Molecular Dynamics Simulations. J Chem Inf Model 2021; 61:2926-2936. [PMID: 34029080 DOI: 10.1021/acs.jcim.1c00200] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Elucidation and improvement of the blood coagulant properties of heparin are the focus of intense research. In this study, we performed conformational analysis using nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics (MD) simulations on the heparin pentasaccharide analogue idraparinux, its disulfonatomethyl analogue, which features a slightly improved blood coagulation property, and a trisulfonatomethyl analogue, in which the activity has been totally abolished. As the ring conformation of the G subunit has been suggested as a major determinant of the biological properties, we analyzed the sugar ring conformations and dynamics of the interglycosidic linkages. We found that the conformation of the G ring is dominated by the 2SO skewed boat next to the 1C4 chair in all three derivatives. Both the thermodynamics and the kinetics of the conformational states were found to be highly similar in the three derivatives. Molecular kinetic analysis showed that the 2SO skewed boat state of the G ring is equally favorable in the three analogues, resulting in similar 2SO populations. Also, the transition kinetics from the 1C4 chair to the 2SO skewed boat was found to be comparable in the derivatives, which indicates a similar energy barrier between the two states of the G subunit. We also identified a slower conformational transition between the dominant 4C1 chair and the boat conformations on the E subunit. Both G and E ring flips are also accompanied by changes along the interglycosidic linkages, which take place highly synchronously with the ring flips. These findings indicate that conformational plasticity of the G ring and the dominance of the 2SO skewed boat populations do not necessarily warrant the biological activity of the derivatives and hence the impact of other factors also needs to be considered.
Collapse
Affiliation(s)
- Gábor Balogh
- Division of Clinical Laboratory Science, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Nagyerdei krt. 98, H-4032 Debrecen, Hungary
| | - Tamás Gyöngyösi
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary.,MTA-DE Molecular Recognition and Interaction Research Group, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - István Timári
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - Mihály Herczeg
- Department of Pharmaceutical Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary.,Research Group for Oligosaccharide Chemistry of Hungarian Academy of Sciences, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - Anikó Borbás
- Department of Pharmaceutical Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - S Kashif Sadiq
- Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.,European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Krisztina Fehér
- MTA-DE Molecular Recognition and Interaction Research Group, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - Katalin E Kövér
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary.,MTA-DE Molecular Recognition and Interaction Research Group, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
| |
Collapse
|
2
|
Nagarajan B, Sankaranarayanan NV, Desai UR. Perspective on computational simulations of glycosaminoglycans. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2019; 9:e1388. [PMID: 31080520 PMCID: PMC6504973 DOI: 10.1002/wcms.1388] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 07/07/2018] [Indexed: 01/06/2023]
Abstract
Glycosaminoglycans (GAGs) represent a formidable frontier for chemists, biochemists, biologists, medicinal chemists and drug delivery specialists because of massive structural complexity. GAGs are arguably the most complex, natural linear biopolymers with theoretical diversity orders of magnitude higher than proteins and nucleic acids. Yet, this diversity remains generally untapped. Computational approaches offer major routes to understand GAG structure and dynamics so as to enable novel applications of these biopolymers. In fact, computational algorithms, softwares, online tools and techniques have reached a level of sophistication that help understand atomistic details of conformational variation and protein recognition of individual GAG sequences. This review describes current approaches and challenges in computational study of GAGs. It presents a history of major findings since the earliest mention of GAGs (the 1960s), the development of parameters and force fields specific for GAGs, and the application of these tools in understanding GAG structure-function relationship. This review also presents a section on how to perform simulation of GAGs, which is directed toward researchers interested in entering this promising field with potential to impact therapy.
Collapse
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
| |
Collapse
|
3
|
Mothéré M, Singabraya D, Driguez PA, Siñeriz F, Papy-Garcia D. Poly(ethylene glycol acrylate)-functionalized hydrogels for heparan sulfate oligosaccharide recognition. J Mol Recognit 2016; 30. [PMID: 27790778 DOI: 10.1002/jmr.2584] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 07/12/2016] [Accepted: 09/14/2016] [Indexed: 02/02/2023]
Abstract
Heparan sulfates are complex polysaccharides belonging to the family of glycosaminoglycans that participate to the regulation of cell behavior and tissue homeostasis. The biological activities conferred to heparan sulfates are largely dependent on the content and positioning of the sulfate groups along their saccharidic units. At present, identification of particular sulfation patterns in biologically relevant heparan sulfate sequences remains challenging. Although several approaches for structure analysis exist, the complexity of heparan sulfates makes new and original approaches still required. Here, we used molecular imprinting technologies to prepare a library of polyethylene glycol acrylate functionalized hydrogels with the aim to investigate their applicability as specific recognizing systems for fondaparinux, a synthetic pentasaccharide analog to the antithrombin binding site of heparin. Adequate choice of the hydrogel composition and controlling rebinding conditions were important determinants for improving the sulfated oligosaccharide recognition specificity and selectivity. Our results suggest that molecular imprinting approaches could be a possibility for the specific recognition of biologically active sequences in heparan sulfates.
Collapse
Affiliation(s)
- Mouna Mothéré
- Laboratoire CRRET ERL CNRS_9215, Université Paris-Est, UPEC, F-94000, Créteil, France
| | - Dominique Singabraya
- Laboratoire CRRET ERL CNRS_9215, Université Paris-Est, UPEC, F-94000, Créteil, France
| | - Pierre-Alexandre Driguez
- Biological Chemistry - Lead Generation and Candidate Realization, Sanofi R&D, 13 Quai Jules Guesde, BP14, 94403, Vitry-sur-Seine Cedex, France
| | | | - Dulce Papy-Garcia
- Laboratoire CRRET ERL CNRS_9215, Université Paris-Est, UPEC, F-94000, Créteil, France
| |
Collapse
|
4
|
Abstract
High-resolution NMR and density functional theory (DFT) calculations have been applied to analysis of heparin pentasaccharide 3D structure in aqueous solution. The fully optimized molecular geometry of two pentasaccharide conformations (differing from each other in the form, one (1)C4 and the other (2)S0, of the sulfated iduronic acid residue) were obtained using the B3LYP/6-311+G(d,p) level of theory in the presence of solvent, the latter included as explicit water molecules. The presented approach enabled insight into variations of the bond lengths, bond angles, and torsion angles, formations of intra- and intermolecular hydrogen bonds, and ionic interactions in the two pentasaccharide conformations. A rather complex hydrogen bond network is formed, including inter-residue and intraresidue bonds between the NH group in the GlcN,3,6S with oxygens linked to C-2 at the IdoA2S residue and the glycosidic O-1 and the neighboring OSO3(-) group linked to C-3 in the same residue. On the other hand, because the first hydration shell is strongly influenced by strong ion-ion and ion-dipole interactions between sodium ions, sulfates, carboxylates, and -OH groups, ionic interactions play an important role in the stabilization of the 3D structure. The DFT-computed three-bond proton-proton coupling constants also showed that best agreement with experiment was obtained with a weighted average of 15:85 ((1)C4/(2)S0) of the sulfated iduronic acid forms indicating that the ratio is even more shifted toward the (2)S0 form than previously supposed. The DFT-computed pentasaccharide conformation differs from the previously published data, with the main changes at the glycosidic linkages, namely, the ψ1 torsion angles and the ϕ3 angle. The comparison of the glycosidic linkage torsion angle values in solution with the antithrombin-pentasaccharide complex also indicates that the pentasaccharide conformation changes upon binding to antithrombin III. The data supports the assumption that the protein selects the more populated (2)S0 conformer of heparin pentasaccharide and, consequently, the binding process of heparin pentasaccharide with antithrombin III is energetically more favorable than formerly expected.
Collapse
Affiliation(s)
- Miloš Hricovíni
- Institute of Chemistry, Slovak Academy of Sciences , 845 38 Bratislava, Slovakia
| |
Collapse
|
5
|
Hricovíni M, Driguez PA, Malkina OL. NMR and DFT analysis of trisaccharide from heparin repeating sequence. J Phys Chem B 2014; 118:11931-42. [PMID: 25254635 DOI: 10.1021/jp508045n] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
NMR and density functional theory (DFT) have afforded detailed information on the molecular geometry and spin-spin coupling constants of a trisaccharide from the heparin repeating-sequence. The fully optimized molecular structures of two trisaccharide conformations (differing from each other in the form of the central iduronic acid residue) were obtained using the B3LYP/6-311+G(d,p) level of theory in the presence of solvent, the latter included as either explicit water molecules or via a continuum solvent model. NMR spin-spin coupling constants were also computed using various basis sets and functionals and then compared with measured experimental values. Optimized structures for both conformers showed differences in geometry at the glycosidic linkages and in the formation of intramolecular hydrogen bonds. Three-bond proton-proton coupling constants ((3)JH-C-C-H), based on fully optimized geometry computed using the B3LYP/6-311+G(d,p)/UFF level of theory and hydrated with 57 water molecules, showed that the best agreement with experiment was obtained with the 6-311+G(d,p) basis set and a weighted average of 55:45 ((1)C4:(2)S0) of the IdoA2S forms. Other basis sets, DGDZVP and TZVP, also gave acceptable data for most coupling constants, with DGDZVP outperforming the TZVP. Detailed analysis of Fermi-contact contributions to (3)JH-C-C-H showed that important contributions arise from oxygen at both glycosidic linkages, as well as from oxygen atoms on the neighboring monosaccharide units. Their contribution to the Fermi term cannot be neglected and must be taken into account for a correct description of coupling constants. The analysis also showed that the magnitude of paramagnetic (PSO) and diamagnetic (DSO) spin-orbit contributions is comparable to the magnitude of the Fermi-contact contribution in some coupling constants in the IdoA2S residue. Calculations of the localized molecular orbital contributions to the DSO terms from separate conformational residues showed that the contribution from adjacent residues is not negligible and can be important for the spin-spin coupling constants between protons located close to the geometrical center of the molecule. These contributions should be taken into account when interpreting DSO terms in spin-spin coupling constants especially in large molecules.
Collapse
Affiliation(s)
- Miloš Hricovíni
- Institute of Chemistry, Slovak Academy of Sciences , 845 38 Bratislava, Slovakia
| | | | | |
Collapse
|
6
|
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]
|
7
|
Chabrol E, Nurisso A, Daina A, Vassal-Stermann E, Thepaut M, Girard E, Vivès RR, Fieschi F. Glycosaminoglycans are interactants of Langerin: comparison with gp120 highlights an unexpected calcium-independent binding mode. PLoS One 2012; 7:e50722. [PMID: 23226363 PMCID: PMC3511376 DOI: 10.1371/journal.pone.0050722] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 10/24/2012] [Indexed: 12/29/2022] Open
Abstract
Langerin is a C-type lectin specifically expressed in Langerhans cells. As recently shown for HIV, Langerin is thought to capture pathogens and mediate their internalisation into Birbeck Granules for elimination. However, the precise functions of Langerin remain elusive, mostly because of the lack of information on its binding properties and physiological ligands. Based on recent reports that Langerin binds to sulfated sugars, we conducted here a comparative analysis of Langerin interaction with mannose-rich HIV glycoprotein gp120 and glycosaminoglycan (GAGs), a family of sulfated polysaccharides expressed at the surface of most mammalian cells. Our results first revealed that Langerin bound to these different glycans through very distinct mechanisms and led to the identification of a novel, GAG-specific binding mode within Langerin. In contrast to the canonical lectin domain, this new binding site showed no Ca(2+)-dependency, and could only be detected in entire, trimeric extracellular domains of Langerin. Interestingly binding to GAGs, did not simply rely on a net charge effect, but rather on more discrete saccharide features, such as 6-O-sulfation, or iduronic acid content. Using molecular modelling simulations, we proposed a model of Langerin/heparin complex, which located the GAG binding site at the interface of two of the three Carbohydrate-recognition domains of the protein, at the edge of the a-helix coiled-coil. To our knowledge, the binding properties that we have highlighted here for Langerin, have never been reported for C-type lectins before. These findings provide new insights towards the understanding of Langerin biological functions.
Collapse
Affiliation(s)
- Eric Chabrol
- Groupe Membrane & Pathogens, Institut de Biologie Structurale, Université Joseph Fourier, Grenoble, France
- UMR 5075, CNRS, Grenoble, France
- Departement des sciences du vivant, CEA, Grenoble, France
| | - Alessandra Nurisso
- Département de Pharmacochimie, Université de Genève, Genève, Switzerland
| | - Antoine Daina
- Département de Pharmacochimie, Université de Genève, Genève, Switzerland
- Molecular Modeling Group, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Emilie Vassal-Stermann
- UMR 5075, CNRS, Grenoble, France
- Departement des sciences du vivant, CEA, Grenoble, France
- Groupe SAGAG, Institut de Biologie Structurale, Université Joseph Fourier, Grenoble, France
| | - Michel Thepaut
- Groupe Membrane & Pathogens, Institut de Biologie Structurale, Université Joseph Fourier, Grenoble, France
- UMR 5075, CNRS, Grenoble, France
- Departement des sciences du vivant, CEA, Grenoble, France
| | - Eric Girard
- UMR 5075, CNRS, Grenoble, France
- Departement des sciences du vivant, CEA, Grenoble, France
- Groupe ELMA, Institut de Biologie Structurale, Université Joseph Fourier, Grenoble, France
| | - Romain R. Vivès
- UMR 5075, CNRS, Grenoble, France
- Departement des sciences du vivant, CEA, Grenoble, France
- Molecular Modeling Group, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Franck Fieschi
- Groupe Membrane & Pathogens, Institut de Biologie Structurale, Université Joseph Fourier, Grenoble, France
- UMR 5075, CNRS, Grenoble, France
- Departement des sciences du vivant, CEA, Grenoble, France
- Institut Universitaire de France, Paris, France
- * E-mail:
| |
Collapse
|
8
|
Lortat-Jacob H, Burhan I, Scarpellini A, Thomas A, Imberty A, Vivès RR, Johnson T, Gutierrez A, Verderio EAM. Transglutaminase-2 interaction with heparin: identification of a heparin binding site that regulates cell adhesion to fibronectin-transglutaminase-2 matrix. J Biol Chem 2012; 287:18005-17. [PMID: 22442151 PMCID: PMC3365763 DOI: 10.1074/jbc.m111.337089] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Heparan sulfate proteoglycans are critical binding partners for extracellular tranglutaminase-2 (TG2), a multifunctional protein involved in tissue remodeling events related to organ fibrosis and cancer progression. We previously showed that TG2 has a strong affinity for heparan sulfate (HS)/heparin and reported that the heparan sulfate proteoglycan syndecan-4 acts as a receptor for TG2 via its HS chains in two ways: by increasing TG2-cell surface trafficking/externalization and by mediating RGD-independent cell adhesion to fibronectin-TG2 matrix during wound healing. Here we have investigated the molecular basis of this interaction. Site-directed mutagenesis revealed that either mutation of basic RRWK (262–265) or KQKRK (598–602) clusters, forming accessible heparin binding sequences on the TG2 three-dimensional structure, led to an almost complete reduction of heparin binding, indicating that both clusters contribute to form a single binding surface. Mutation of residues Arg19 and Arg28 also led to a significant reduction in heparin binding, suggesting their involvement. Our findings indicate that the heparin binding sites on TG2 mainly comprise two clusters of basic amino acids, which are distant in the linear sequence but brought into spatial proximity in the folded “closed” protein, forming a high affinity heparin binding site. Molecular modeling showed that the identified site can make contact with a single heparin-derived pentasaccharide. The TG2-heparin binding mutants supported only weak RGD-independent cell adhesion compared with wild type TG2 or mutants with retained heparin binding, and both heparin binding clusters were critical for TG2-mediated cell adhesion. These findings significantly advance our knowledge of how HS/heparin influences the adhesive function of TG2.
Collapse
Affiliation(s)
- Hugues Lortat-Jacob
- CNRS-Commissariat à l'Energie Atomique-Université Joseph Fourier, Grenoble 1, Institut de Biologie Structurale Jean-Pierre Ebel, Grenoble, France.
| | | | | | | | | | | | | | | | | |
Collapse
|
9
|
Delattre C, Chaisemartin L, Favre-Mercuret M, Berthon J, Rios L. Biological effect of β-(1,3)-polyglucuronic acid sodium salt on lipid storage and adipocytes differentiation. Carbohydr Polym 2012; 87:775-783. [DOI: 10.1016/j.carbpol.2011.08.056] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2011] [Revised: 08/13/2011] [Accepted: 08/21/2011] [Indexed: 11/24/2022]
|
10
|
Tran VM, Nguyen TKN, Raman K, Kuberan B. Applications of isotopes in advancing structural and functional heparanomics. Anal Bioanal Chem 2010; 399:559-70. [PMID: 20838780 DOI: 10.1007/s00216-010-4166-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Revised: 08/23/2010] [Accepted: 08/24/2010] [Indexed: 12/11/2022]
Abstract
Heparanomics is the study of all the biologically active oligosaccharide domain structures in the entire heparanome and the nature of the interactions among these domains and their protein ligands. Structural elucidation of heparan sulfate and heparin oligosaccharides is a major obstacle in advancing structure-function relationships and heparanomics. There are several factors that exacerbate the challenges involved in the structural elucidation of heparin and heparan sulfate; therefore, there is great interest in developing novel strategies and analytical tools to overcome the barriers in decoding the enigmatic heparanome. This review focuses on the applications of isotopes, both radioisotopes and stable isotopes, in the structural elucidation of the complex heparanome at the disaccharide or oligosaccharide level using liquid chromatography, nuclear magnetic resonance spectroscopy, and mass spectrometry. This review also outlines the utility of isotopes in determining the substrate specificity of biosynthetic enzymes that eventually dictate the emergence of biologically active oligosaccharides.
Collapse
Affiliation(s)
- Vy M Tran
- Department of Bioengineering, University of Utah, Salt Lake City, UT 84112, USA
| | | | | | | |
Collapse
|
11
|
Synthesis and conformational analysis of carbasugar bioisosteres of α-l-iduronic acid and its methyl glycoside. Carbohydr Res 2010; 345:984-93. [DOI: 10.1016/j.carres.2010.03.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Revised: 02/15/2010] [Accepted: 03/01/2010] [Indexed: 11/18/2022]
|
12
|
Sigulinsky C, Babu P, Victor XV, Kuberan B. Preparation and characterization of (15)N-enriched, size-defined heparan sulfate precursor oligosaccharides. Carbohydr Res 2010; 345:250-6. [PMID: 19945695 PMCID: PMC2812664 DOI: 10.1016/j.carres.2009.10.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2009] [Revised: 10/22/2009] [Accepted: 10/28/2009] [Indexed: 11/26/2022]
Abstract
We report the preparation of size-defined [(15)N]N-acetylheparosan oligosaccharides from Escherichia coli-derived (15)N-enriched N-acetylheparosan. Optimized growth conditions of E. coli in minimal media containing (15)NH(4)Cl yielded [(15)N]N-acetylheparosan on a preparative scale. Depolymerization of [(15)N]N-acetylheparosan by heparitinase I yielded resolvable, even-numbered oligosaccharides ranging from disaccharide to icosaccharide. Anion-exchange chromatography-assisted fractionation afforded size-defined [(15)N]N-acetylheparosan oligosaccharides identifiable by ESI-TOFMS. These isotopically labeled oligosaccharides will prove to be valuable research tools for the chemoenzymatic synthesis of heparin and heparan sulfate oligosaccharides and for the study of their structural biology.
Collapse
Affiliation(s)
- Crystal Sigulinsky
- Interdepartmental Program in Neuroscience, University of Utah, Salt Lake City, Utah, 84112, USA
| | - Ponnusamy Babu
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah, 84112, USA
| | - Xylophone V. Victor
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah, 84112, USA
| | - Balagurunathan Kuberan
- Interdepartmental Program in Neuroscience, University of Utah, Salt Lake City, Utah, 84112, USA
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah, 84112, USA
- Department of Bioengineering, University of Utah, Salt Lake City, Utah, 84112, USA
| |
Collapse
|
13
|
Guglieri S, Hricovíni M, Raman R, Polito L, Torri G, Casu B, Sasisekharan R, Guerrini M. Minimum FGF2 Binding Structural Requirements of Heparin and Heparan Sulfate Oligosaccharides As Determined by NMR Spectroscopy. Biochemistry 2008; 47:13862-9. [DOI: 10.1021/bi801007p] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sara Guglieri
- G. Ronzoni Institute for Chemical and Biochemical Research, Milan, Italy, Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia, Department of Biological Engineering, Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, and Department of Organic and Industrial Chemistry, University of Milan, Milan, Italy
| | - Miloš Hricovíni
- G. Ronzoni Institute for Chemical and Biochemical Research, Milan, Italy, Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia, Department of Biological Engineering, Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, and Department of Organic and Industrial Chemistry, University of Milan, Milan, Italy
| | - Rahul Raman
- G. Ronzoni Institute for Chemical and Biochemical Research, Milan, Italy, Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia, Department of Biological Engineering, Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, and Department of Organic and Industrial Chemistry, University of Milan, Milan, Italy
| | - Laura Polito
- G. Ronzoni Institute for Chemical and Biochemical Research, Milan, Italy, Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia, Department of Biological Engineering, Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, and Department of Organic and Industrial Chemistry, University of Milan, Milan, Italy
| | - Giangiacomo Torri
- G. Ronzoni Institute for Chemical and Biochemical Research, Milan, Italy, Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia, Department of Biological Engineering, Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, and Department of Organic and Industrial Chemistry, University of Milan, Milan, Italy
| | - Benito Casu
- G. Ronzoni Institute for Chemical and Biochemical Research, Milan, Italy, Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia, Department of Biological Engineering, Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, and Department of Organic and Industrial Chemistry, University of Milan, Milan, Italy
| | - Ram Sasisekharan
- G. Ronzoni Institute for Chemical and Biochemical Research, Milan, Italy, Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia, Department of Biological Engineering, Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, and Department of Organic and Industrial Chemistry, University of Milan, Milan, Italy
| | - Marco Guerrini
- G. Ronzoni Institute for Chemical and Biochemical Research, Milan, Italy, Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia, Department of Biological Engineering, Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, and Department of Organic and Industrial Chemistry, University of Milan, Milan, Italy
| |
Collapse
|
14
|
Abstract
We have a limited understanding of the details of molecular recognition of carbohydrates by proteins, which is critical to a multitude of biological processes. Furthermore, carbohydrate-modifying proteins such as glycosyl hydrolases and phosphorylases are of growing importance as potential drug targets. Interactions between proteins and carbohydrates have complex thermodynamics, and in general the specific positioning of only a few hydroxyl groups determines their binding affinities. A thorough understanding of both carbohydrate and protein structures is thus essential to predict these interactions. An atomic-level view of carbohydrate recognition through structures of carbohydrate-active enzymes complexed with transition-state inhibitors reveals some of the distinctive molecular features unique to protein-carbohydrate complexes. However, the inherent flexibility of carbohydrates and their often water-mediated hydrogen bonding to proteins makes simulation of their complexes difficult. Nonetheless, recent developments such as the parameterization of specific force fields and docking scoring functions have greatly improved our ability to predict protein-carbohydrate interactions. We review protein-carbohydrate complexes having defined molecular requirements for specific carbohydrate recognition by proteins, providing an overview of the different computational techniques available to model them.
Collapse
Affiliation(s)
- Alain Laederach
- Department of Chemical Engineering, Iowa State University, Ames, Iowa 50011-2230, USA
| | | |
Collapse
|
15
|
Vivès RR, Imberty A, Sattentau QJ, Lortat-Jacob H. Heparan sulfate targets the HIV-1 envelope glycoprotein gp120 coreceptor binding site. J Biol Chem 2005; 280:21353-7. [PMID: 15797855 DOI: 10.1074/jbc.m500911200] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human immunodeficiency virus (HIV) attachment to host cells is a multi-step process that involves interaction of the viral envelope gp120 with the primary receptor CD4 and coreceptors. HIV gp120 also binds to other cell surface components, including heparan sulfate (HS), a sulfated polysaccharide whose wide interactive properties are exploited by many pathogens for attachment and concentration at the cell surface. To analyze the structural features of gp120 binding to HS, we used soluble CD4 to constrain gp120 in a specific conformation. We first found that CD4 induced conformational change of gp120, dramatically increasing binding to HS. We then showed that HS binding interface on gp120 comprised, in addition to the well characterized V3 loop, a CD4-induced epitope. This epitope is efficiently targeted by nanomolar concentrations of size-defined heparin/HS-derived oligosaccharides. Because this domain of the protein also constitutes the binding site for the viral coreceptors, these results support an implication of HS at late stages of the virus-cell attachment process and suggest potential therapeutic applications.
Collapse
Affiliation(s)
- Romain R Vivès
- Institut de Biologie Structurale, CNRS-Commissariat à l'Energie Atomique-Université Joseph Fourier, UMR 5075, 41 Rue Horowitz, 38027 Grenoble, France
| | | | | | | |
Collapse
|
16
|
Verli H, Guimarães JA. Molecular dynamics simulation of a decasaccharide fragment of heparin in aqueous solution. Carbohydr Res 2004; 339:281-90. [PMID: 14698886 DOI: 10.1016/j.carres.2003.09.026] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Molecular dynamics (MD) simulations on heparin-water-sodium systems were carried out in order to establish a simulation protocol able to represent heparin solution conformation under physiological conditions. Atomic charges suitable for heparin oligosaccharides were obtained from ab initio quantum-mechanical computations, at the 6-31G(**) level. The GROMACS forcefield, the SPC, and SPC/E water models were employed. Also heparin was simulated with IdoA residues in 1C(4) or 2S(0) conformational states. The results of the performed MD simulations are in agreement with the available experimental data, suggesting that this approach can be applied for the study of heparin interactions with its target proteins and thus play a role in the development of new antithrombotic agents.
Collapse
Affiliation(s)
- Hugo Verli
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, 9500, CP 15005, 91500-970, RS, Porto Alegre, Brazil
| | | |
Collapse
|
17
|
Casu B, Lindahl U. Structure and biological interactions of heparin and heparan sulfate. Adv Carbohydr Chem Biochem 2002; 57:159-206. [PMID: 11836942 DOI: 10.1016/s0065-2318(01)57017-1] [Citation(s) in RCA: 296] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- B Casu
- G. Ronzoni Institute for Chemical and Biochemical Research, Milan, Italy
| | | |
Collapse
|
18
|
Abstract
Regioselective derivatization was carried out introducing sulfate, phosphate or quaternary ammonia groups in C2-, C3- and C6-position of the anhydroglycose unit of cellulose. The anticoagulant potential of these derivatives was estimated with common clotting assays, such as thrombin time and partial thromboplastin time. It was found that a pronounced anticoagulant activity of cellulose derivatives could be achieved if the degree of substitution (DS) with sulfate was above 1.0. The anticoagulant activity was maximal at a DS of about 1.5 and then decreased again. Further, it was detected that particularly sulfation in C2-position resulted in a pronounced anticoagulant activity of cellulose derivatives. Development and application of assays specific for thrombin and factor Xa indicated that the anticoagulant potential of these cellulose derivatives was mainly due to anti-thrombin activity. The comparison of cellulose sulfates and cellulose derivatized with phosphate and quaternary ammonium groups demonstrated that the negative charge and type of the substituent is an important prerequisite for the anticoagulant activity of cellulose derivatives. Indeed, derivatization with sulfate produced superior activity in comparison with phosphate.
Collapse
Affiliation(s)
- T Groth
- Department of Membrane Research, Institute of Chemistry, GKSS Research Center, Teltow, Germany.
| | | |
Collapse
|
19
|
Sadir R, Baleux F, Grosdidier A, Imberty A, Lortat-Jacob H. Characterization of the stromal cell-derived factor-1alpha-heparin complex. J Biol Chem 2001; 276:8288-96. [PMID: 11087743 DOI: 10.1074/jbc.m008110200] [Citation(s) in RCA: 175] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The binding of chemokines to glycosaminoglycans is thought to play a crucial role in chemokine functions. It has recently been shown that stromal cell-derived factor-1alpha (SDF-1alpha), a CXC chemokine with potent anti-human immunodeficiency virus activity, binds to heparan sulfate through a typical consensus sequence for heparin recognition (BBXB, where B is a basic residue KHLK, amino acids 24-27). Calculation of the accessible surface, together with the electrostatic potential of the SDF-1alpha dimer, revealed that other amino acids (Arg-41 and Lys-43) are found in the same surface area and contribute to the creation of a positively charged crevice, located at the dimer interface. GRID calculations confirmed that this binding site will be the most energetically favored area for the interaction with sulfate groups. Site-directed mutagenesis and surface plasmon resonance-based binding assays were used to investigate the structural basis for SDF-1alpha binding to heparin. Among the residues clustered in this basic surface area, Lys-24 and Lys-27 have dominant roles and are essential for interaction with heparin. Amino acids Arg-41 and Lys-43 participate in the binding but are not strictly required for the interaction to take place. Direct binding assays and competition analysis with monoclonal antibodies also permitted us to show that the N-terminal residue (Lys-1), an amino acid critical for receptor activation, is involved in complex formation. Binding studies with selectively desulfated heparin, heparin oligosaccharides, and heparitinase-resistant heparan sulfate fragments showed that a minimum size of 12-14 monosaccharide units is required for efficient binding and that 2-O- and N-sulfate groups have a dominant role in the interaction. Finally, the heparin-binding site was identified on the crystal structure of SDF-1alpha, and a docking study was undertaken. During the energy minimization process, heparin lost its perfect ribbon shape and fitted the protein surface perfectly. In the model, Lys-1, Lys-24, Lys-27, and Arg-41 were found to have the major role in binding a polysaccharide fragment consisting of 13 monosaccharide units.
Collapse
Affiliation(s)
- R Sadir
- Institut de Biologie Structurale, CNRS-CEA-UJF, Laboratoire de Biophysique Moléculaire, 41 Rue Horowitz, 38027 Grenoble Cedex 01, France
| | | | | | | | | |
Collapse
|
20
|
Imberty A, Pérez S. Structure, conformation, and dynamics of bioactive oligosaccharides: theoretical approaches and experimental validations. Chem Rev 2000; 100:4567-88. [PMID: 11749358 DOI: 10.1021/cr990343j] [Citation(s) in RCA: 212] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- A Imberty
- Centre de Recherches sur les Macromolécules Végétales (CERMAV-CNRS, affiliated with Joseph Fourier Université), 601 rue de la Chimie, BP 53, F-38041 Grenoble Cedex 9
| | | |
Collapse
|