1
|
Fittolani G, Tyrikos-Ergas T, Poveda A, Yu Y, Yadav N, Seeberger PH, Jiménez-Barbero J, Delbianco M. Synthesis of a glycan hairpin. Nat Chem 2023; 15:1461-1469. [PMID: 37400598 PMCID: PMC10533408 DOI: 10.1038/s41557-023-01255-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 05/26/2023] [Indexed: 07/05/2023]
Abstract
The primary sequence of a biopolymer encodes the essential information for folding, permitting to carry out sophisticated functions. Inspired by natural biopolymers, peptide and nucleic acid sequences have been designed to adopt particular three-dimensional (3D) shapes and programmed to exert specific functions. In contrast, synthetic glycans capable of autonomously folding into defined 3D conformations have so far not been explored owing to their structural complexity and lack of design rules. Here we generate a glycan that adopts a stable secondary structure not present in nature, a glycan hairpin, by combining natural glycan motifs, stabilized by a non-conventional hydrogen bond and hydrophobic interactions. Automated glycan assembly enabled rapid access to synthetic analogues, including site-specific 13C-labelled ones, for nuclear magnetic resonance conformational analysis. Long-range inter-residue nuclear Overhauser effects unequivocally confirmed the folded conformation of the synthetic glycan hairpin. The capacity to control the 3D shape across the pool of available monosaccharides has the potential to afford more foldamer scaffolds with programmable properties and functions.
Collapse
Affiliation(s)
- Giulio Fittolani
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Theodore Tyrikos-Ergas
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
- Department of Chemistry, University of Illinois, Urbana, IL, USA
| | - Ana Poveda
- CICbioGUNE, Basque Research and Technology Alliance, Derio, Spain
| | - Yang Yu
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
- Simpson Querrey Institute, Northwestern University, Evanston, IL, USA
| | - Nishu Yadav
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Peter H Seeberger
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Jesús Jiménez-Barbero
- CICbioGUNE, Basque Research and Technology Alliance, Derio, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
- Department of Organic Chemistry II, Faculty of Science and Technology, University of the Basque Country, Leioa, Spain
- Centro de Investigación Biomedica en Red de Enfermedades Respiratorias, Madrid, Spain
| | - Martina Delbianco
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany.
| |
Collapse
|
2
|
Roy R, Poddar S, Kar P. Comparison of the conformational dynamics of an N-glycan in implicit and explicit solvents. Carbohydr Res 2022; 522:108700. [DOI: 10.1016/j.carres.2022.108700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 09/30/2022] [Accepted: 10/03/2022] [Indexed: 11/28/2022]
|
3
|
Abstract
Glycoscience assembles all the scientific disciplines involved in studying various molecules and macromolecules containing carbohydrates and complex glycans. Such an ensemble involves one of the most extensive sets of molecules in quantity and occurrence since they occur in all microorganisms and higher organisms. Once the compositions and sequences of these molecules are established, the determination of their three-dimensional structural and dynamical features is a step toward understanding the molecular basis underlying their properties and functions. The range of the relevant computational methods capable of addressing such issues is anchored by the specificity of stereoelectronic effects from quantum chemistry to mesoscale modeling throughout molecular dynamics and mechanics and coarse-grained and docking calculations. The Review leads the reader through the detailed presentations of the applications of computational modeling. The illustrations cover carbohydrate-carbohydrate interactions, glycolipids, and N- and O-linked glycans, emphasizing their role in SARS-CoV-2. The presentation continues with the structure of polysaccharides in solution and solid-state and lipopolysaccharides in membranes. The full range of protein-carbohydrate interactions is presented, as exemplified by carbohydrate-active enzymes, transporters, lectins, antibodies, and glycosaminoglycan binding proteins. A final section features a list of 150 tools and databases to help address the many issues of structural glycobioinformatics.
Collapse
Affiliation(s)
- Serge Perez
- Centre de Recherche sur les Macromolecules Vegetales, University of Grenoble-Alpes, Centre National de la Recherche Scientifique, Grenoble F-38041, France
| | - Olga Makshakova
- FRC Kazan Scientific Center of Russian Academy of Sciences, Kazan Institute of Biochemistry and Biophysics, Kazan 420111, Russia
| |
Collapse
|
4
|
Fadda E. Molecular simulations of complex carbohydrates and glycoconjugates. Curr Opin Chem Biol 2022; 69:102175. [PMID: 35728307 DOI: 10.1016/j.cbpa.2022.102175] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 11/17/2022]
Abstract
Complex carbohydrates (glycans) are the most abundant and versatile biopolymers in nature. The broad diversity of biochemical functions that carbohydrates cover is a direct consequence of the variety of 3D architectures they can adopt, displaying branched or linear arrangements, widely ranging in sizes, and with the highest diversity of building blocks of any other natural biopolymer. Despite this unparalleled complexity, a common denominator can be found in the glycans' inherent flexibility, which hinders experimental characterization, but that can be addressed by high-performance computing (HPC)-based molecular simulations. In this short review, I present and discuss the state-of-the-art of molecular simulations of complex carbohydrates and glycoconjugates, highlighting methodological strengths and weaknesses, important insights through emblematic case studies, and suggesting perspectives for future developments.
Collapse
Affiliation(s)
- Elisa Fadda
- Department of Chemistry and Hamilton Institute, Maynooth University, Ireland.
| |
Collapse
|
5
|
Fadda E. Understanding the Structure and Function of Viral Glycosylation by Molecular Simulations: State-of-the-Art and Recent Case Studies. COMPREHENSIVE GLYCOSCIENCE 2021. [PMCID: PMC7834635 DOI: 10.1016/b978-0-12-819475-1.00056-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
6
|
Abstract
The conformation of a molecule strongly affects its function, as demonstrated for peptides and nucleic acids. This correlation is much less established for carbohydrates, the most abundant organic materials in nature. Recent advances in synthetic and analytical techniques have enabled the study of carbohydrates at the molecular level. Recurrent structural features were identified as responsible for particular biological activities or material properties. In this Minireview, recent achievements in the structural characterization of carbohydrates, enabled by systematic studies of chemically defined oligosaccharides, are discussed. These findings can guide the development of more potent glycomimetics. Synthetic carbohydrate materials by design can be envisioned.
Collapse
Affiliation(s)
- Yang Yu
- Department of Biomolecular SystemsMax-Planck-Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
- Department of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
| | - Martina Delbianco
- Department of Biomolecular SystemsMax-Planck-Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
| |
Collapse
|
7
|
Roy R, Ghosh B, Kar P. Investigating Conformational Dynamics of Lewis Y Oligosaccharides and Elucidating Blood Group Dependency of Cholera Using Molecular Dynamics. ACS OMEGA 2020; 5:3932-3942. [PMID: 32149220 PMCID: PMC7057322 DOI: 10.1021/acsomega.9b03398] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 02/11/2020] [Indexed: 05/08/2023]
Abstract
Cholera is caused by Vibrio cholerae and is an example of a blood-group-dependent disease. Recent studies suggest that the receptor-binding B subunit of the cholera toxin (CT) binds histo-blood group antigens at a secondary binding site. Herein, we studied the conformational dynamics of Lewis Y (LeY) oligosaccharides, H-tetrasaccharides and A-pentasaccharides, in aqueous solution by conducting accelerated molecular dynamics (aMD) simulations. The flexible nature of both oligosaccharides was displayed in aMD simulations. Furthermore, aMD simulations revealed that for both oligosaccharides in the free form, 4C1 and 1C4 puckers were sampled for all but GalNAc monosaccharides, while either the 4C1 (GlcNAc, Gal, GalNAc) or 1C4 (Fuc2, Fuc3) pucker was sampled in the CT-bound forms. In aMD, the complete transition from the 4C1 to 1C4 pucker was sampled for GlcNAc and Gal in both oligosaccharides. Further, we have observed a transition from the open to closed conformer in the case of A-pentasaccharide, while H-tetrasaccharide remains in the open conformation throughout the simulation. Both oligosaccharides adopted an open conformation in the CT binding site. Moreover, we have investigated the molecular basis of recognition of LeY oligosaccharides by the B subunit of the cholera toxin of classical and El Tor biotypes using the molecular mechanics generalized Born surface area (MM/GBSA) scheme. The O blood group determinant, H-tetrasaccharide, exhibits a stronger affinity to both biotypes compared to the A blood group determinant, A-pentasaccharide, which agrees with the experimental data. The difference in binding free energy between O and A blood group determinants mainly arises due to the increased entropic cost and desolvation energy in the case of A-pentasaccharide compared to that of H-tetrasaccharide. Our study also reveals that the terminal Fuc3 contributes most to the binding free energy compared to other carbohydrate residues as it forms multiple hydrogen bonds with CT. Overall, our study might help in designing glycomimetic drugs targeting the cholera toxin.
Collapse
Affiliation(s)
- Rajarshi Roy
- Discipline
of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Indore 453552, India
| | - Biplab Ghosh
- High
Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - Parimal Kar
- Discipline
of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Indore 453552, India
- E-mail: . Phone: +91 731 2438700 (ext. 550)
| |
Collapse
|
8
|
Alibay I, Bryce RA. Ring Puckering Landscapes of Glycosaminoglycan-Related Monosaccharides from Molecular Dynamics Simulations. J Chem Inf Model 2019; 59:4729-4741. [PMID: 31609614 DOI: 10.1021/acs.jcim.9b00529] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The conformational flexibility of the glycosaminoglycans (GAGs) is known to be key in their binding and biological function, for example in regulating coagulation and cell growth. In this work, we employ enhanced sampling molecular dynamics simulations to probe the ring conformations of GAG-related monosaccharides, including a range of acetylated and sulfated GAG residues. We first perform unbiased MD simulations of glucose anomers and the epimers glucuronate and iduronate. These calculations indicate that in some cases, an excess of 15 μs is required for adequate sampling of ring pucker due to the high energy barriers between states. However, by applying our recently developed msesMD simulation method (multidimensional swarm-enhanced sampling molecular dynamics), we were able to quantitatively and rapidly reproduce these ring pucker landscapes. From msesMD simulations, the puckering free energy profiles were then compared for 15 further monosaccharides related to GAGs; this includes to our knowledge the first simulation study of sulfation effects on β-GalNAc ring puckering. For the force field employed, we find that in general the calculated pucker free energy profiles for sulfated sugars were similar to the corresponding unsulfated profiles. This accords with recent experimental studies suggesting that variation in ring pucker of sulfated GAG residues is primarily dictated by interactions with surrounding residues rather than by intrinsic conformational preference. As an exception to this, however, we predict that 4-O-sulfation of β-GalNAc leads to reduced ring rigidity, with a significant lowering in energy of the 1C4 ring conformation; this observation may have implications for understanding the structural basis of the biological function of β-GalNAc-containing glycosaminoglycans such as dermatan sulfate.
Collapse
Affiliation(s)
- Irfan Alibay
- Division of Pharmacy and Optometry, School of Health Sciences , University of Manchester , Oxford Road , Manchester M13 9PT , U.K.,Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry , University of Oxford , South Parks Road , Oxford OX1 3QU , U.K
| | - Richard A Bryce
- Division of Pharmacy and Optometry, School of Health Sciences , University of Manchester , Oxford Road , Manchester M13 9PT , U.K
| |
Collapse
|
9
|
Suzuki T, Yanaka S, Watanabe T, Yan G, Satoh T, Yagi H, Yamaguchi T, Kato K. Remodeling of the Oligosaccharide Conformational Space in the Prebound State To Improve Lectin-Binding Affinity. Biochemistry 2019; 59:3180-3185. [PMID: 31553574 DOI: 10.1021/acs.biochem.9b00594] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We developed an approach to improve the lectin-binding affinity of an oligosaccharide by remodeling its conformational space in the precomplexed state. To develop this approach, we used a Lewis X-containing oligosaccharide interacting with RSL as a model system. Using an experimentally validated molecular dynamics simulation, we designed a Lewis X analogue with an increased population of conformational species that were originally very minor but exclusively accessible to the target lectin without steric hindrance by modifying the nonreducing terminal galactose, which does not directly contact the lectin in the complex. This Lewis X mimetic showed 17 times higher affinity for the lectin than the native counterpart. Our approach, complementing the lectin-bound-state optimizations, offers an alternative strategy to create high-affinity oligosaccharides by increasing populations of on-pathway metastable conformers.
Collapse
Affiliation(s)
- Tatsuya Suzuki
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan.,Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan.,Faculty and Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| | - Saeko Yanaka
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan.,Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan.,Faculty and Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan.,School of Physical Sciences, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
| | - Tokio Watanabe
- Faculty and Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| | - Gengwei Yan
- Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan.,School of Physical Sciences, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan.,School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi 923-1292, Japan
| | - Tadashi Satoh
- Faculty and Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| | - Hirokazu Yagi
- Faculty and Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| | - Takumi Yamaguchi
- Faculty and Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan.,School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi 923-1292, Japan
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan.,Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan.,Faculty and Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan.,School of Physical Sciences, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
| |
Collapse
|
10
|
Pandey P, Aytenfisu AH, MacKerell AD, Mallajosyula SS. Drude Polarizable Force Field Parametrization of Carboxylate and N-Acetyl Amine Carbohydrate Derivatives. J Chem Theory Comput 2019; 15:4982-5000. [PMID: 31411469 PMCID: PMC6852669 DOI: 10.1021/acs.jctc.9b00327] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In this work, we report the development of Drude polarizable force field parameters for the carboxylate and N-acetyl amine derivatives, extending the functionality of the existing Drude polarizable carbohydrate force field. The force field parameters have been developed in a hierarchical manner, reproducing the quantum mechanical gas-phase properties of small model compounds representing the key functional group in the carbohydrate derivatives, including optimization of the electrostatic and bonded parameters. The optimized parameters were then used to generate the models for carboxylate and N-acetyl amine carbohydrate derivatives. The transferred parameters were further tested and optimized to reproduce crystal geometries and J-coupling data from nuclear magnetic resonance experiments. The parameter development resulted in the incorporation of d-glucuronate, l-iduronate, N-acetyl-d-glucosamine (GlcNAc), and N-acetyl-d-galactosamine (GalNAc) sugars into the Drude polarizable force field. The parameters developed in this study were then applied to study the conformational properties of glycosaminoglycan polymer hyaluronan, composed of d-glucuronate and N-acetyl-d-glucosamine, in aqueous solution. Upon comparing the results from the additive and polarizable simulations, it was found that the inclusion of polarization improved the description of the electrostatic interactions observed in hyaluronan, resulting in enhanced conformational flexibility. The developed Drude polarizable force field parameters in conjunction with the remainder of the Drude polarizable force field parameters can be used for future studies involving carbohydrates and their conjugates in complex, heterogeneous systems.
Collapse
Affiliation(s)
| | - Asaminew H Aytenfisu
- Department of Pharmaceutical Sciences , University of Maryland School of Pharmacy , 20 Penn Street , Baltimore , Maryland 21201 , United States
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences , University of Maryland School of Pharmacy , 20 Penn Street , Baltimore , Maryland 21201 , United States
| | | |
Collapse
|
11
|
Lepsik M, Sommer R, Kuhaudomlarp S, Lelimousin M, Paci E, Varrot A, Titz A, Imberty A. Induction of rare conformation of oligosaccharide by binding to calcium-dependent bacterial lectin: X-ray crystallography and modelling study. Eur J Med Chem 2019; 177:212-220. [PMID: 31146126 DOI: 10.1016/j.ejmech.2019.05.049] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 05/17/2019] [Accepted: 05/17/2019] [Indexed: 11/29/2022]
Abstract
Pathogenic micro-organisms utilize protein receptors (lectins) in adhesion to host tissues, a process that in some cases relies on the interaction between lectins and human glycoconjugates. Oligosaccharide epitopes are recognized through their three-dimensional structure and their flexibility is a key issue in specificity. In this paper, we analysed by X-ray crystallography the structures of the LecB lectin from two strains of Pseudomonas aeruginosa in complex with Lewis x oligosaccharide present on cell surfaces of human tissues. An unusual conformation of the glycan was observed in all binding sites with a non-canonical syn orientation of the N-acetyl group of N-acetyl-glucosamine. A PDB-wide search revealed that such an orientation occurs only in 4% of protein/carbohydrate complexes. Theoretical chemistry calculations showed that the observed conformation is unstable in solution but stabilised by the lectin. A reliable description of LecB/Lewis x complex by force field-based methods had proven especially challenging due to the special feature of the binding site, two closely apposed Ca2+ ions which induce strong charge delocalisation. By comparing various force-field parametrisations, we propose a general strategy which will be useful in near future for designing carbohydrate-based ligands (glycodrugs) against other calcium-dependent protein receptors.
Collapse
Affiliation(s)
- Martin Lepsik
- Université Grenoble Alpes, CNRS, CERMAV, 38000, Grenoble, France.
| | - Roman Sommer
- Chemical Biology of Carbohydrates, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, D-66123, Saarbrücken, Germany; Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hannover-Braunschweig, Germany; Department of Pharmacy, Saarland University, D-66123, Saarbrücken, Germany
| | | | | | - Emanuele Paci
- Astbury Centre & School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - Annabelle Varrot
- Université Grenoble Alpes, CNRS, CERMAV, 38000, Grenoble, France
| | - Alexander Titz
- Chemical Biology of Carbohydrates, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, D-66123, Saarbrücken, Germany; Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hannover-Braunschweig, Germany; Department of Pharmacy, Saarland University, D-66123, Saarbrücken, Germany
| | - Anne Imberty
- Université Grenoble Alpes, CNRS, CERMAV, 38000, Grenoble, France.
| |
Collapse
|
12
|
Gimeno A, Delgado S, Valverde P, Bertuzzi S, Berbís MA, Echavarren J, Lacetera A, Martín‐Santamaría S, Surolia A, Cañada FJ, Jiménez‐Barbero J, Ardá A. Minimizing the Entropy Penalty for Ligand Binding: Lessons from the Molecular Recognition of the Histo Blood‐Group Antigens by Human Galectin‐3. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201900723] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Ana Gimeno
- CIC bioGUNE Bizkaia Technology Park, Building 800 48160 Derio Bizkaia Spain
| | - Sandra Delgado
- CIC bioGUNE Bizkaia Technology Park, Building 800 48160 Derio Bizkaia Spain
| | - Pablo Valverde
- CIC bioGUNE Bizkaia Technology Park, Building 800 48160 Derio Bizkaia Spain
| | - Sara Bertuzzi
- CIC bioGUNE Bizkaia Technology Park, Building 800 48160 Derio Bizkaia Spain
| | | | - Javier Echavarren
- Centro de Investigaciones Biológicas-CSIC Ramiro de Maeztu 9 28040 Madrid Spain
| | - Alessandra Lacetera
- Centro de Investigaciones Biológicas-CSIC Ramiro de Maeztu 9 28040 Madrid Spain
| | | | | | | | - Jesus Jiménez‐Barbero
- CIC bioGUNE Bizkaia Technology Park, Building 800 48160 Derio Bizkaia Spain
- IkerbasqueBasque Foundation for Science Maria Diaz de Haro 3 48013 Bilbao Bizkaia Spain
- Department of Organic Chemistry, II Faculty of Science and TechnologyUniversity of the Basque Country, EHU-UPV Leioa Spain
| | - Ana Ardá
- CIC bioGUNE Bizkaia Technology Park, Building 800 48160 Derio Bizkaia Spain
| |
Collapse
|
13
|
Gimeno A, Delgado S, Valverde P, Bertuzzi S, Berbís MA, Echavarren J, Lacetera A, Martín-Santamaría S, Surolia A, Cañada FJ, Jiménez-Barbero J, Ardá A. Minimizing the Entropy Penalty for Ligand Binding: Lessons from the Molecular Recognition of the Histo Blood-Group Antigens by Human Galectin-3. Angew Chem Int Ed Engl 2019; 58:7268-7272. [PMID: 30942512 PMCID: PMC6619289 DOI: 10.1002/anie.201900723] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Indexed: 12/13/2022]
Abstract
Ligand conformational entropy plays an important role in carbohydrate recognition events. Glycans are characterized by intrinsic flexibility around the glycosidic linkages, thus in most cases, loss of conformational entropy of the sugar upon complex formation strongly affects the entropy of the binding process. By employing a multidisciplinary approach combining structural, conformational, binding energy, and kinetic information, we investigated the role of conformational entropy in the recognition of the histo blood‐group antigens A and B by human galectin‐3, a lectin of biomedical interest. We show that these rigid natural antigens are pre‐organized ligands for hGal‐3, and that restriction of the conformational flexibility by the branched fucose (Fuc) residue modulates the thermodynamics and kinetics of the binding process. These results highlight the importance of glycan flexibility and provide inspiration for the design of high‐affinity ligands as antagonists for lectins.
Collapse
Affiliation(s)
- Ana Gimeno
- CIC bioGUNE, Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain
| | - Sandra Delgado
- CIC bioGUNE, Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain
| | - Pablo Valverde
- CIC bioGUNE, Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain
| | - Sara Bertuzzi
- CIC bioGUNE, Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain
| | - Manuel Alvaro Berbís
- Centro de Investigaciones Biológicas-CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Javier Echavarren
- Centro de Investigaciones Biológicas-CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Alessandra Lacetera
- Centro de Investigaciones Biológicas-CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | | | | | | | - Jesus Jiménez-Barbero
- CIC bioGUNE, Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain.,Ikerbasque, Basque Foundation for Science, Maria Diaz de Haro 3, 48013, Bilbao, Bizkaia, Spain.,Department of Organic Chemistry, II Faculty of Science and Technology, University of the Basque Country, EHU-UPV, Leioa, Spain
| | - Ana Ardá
- CIC bioGUNE, Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain
| |
Collapse
|
14
|
Bücher KS, Konietzny PB, Snyder NL, Hartmann L. Heteromultivalent Glycooligomers as Mimetics of Blood Group Antigens. Chemistry 2019; 25:3301-3309. [PMID: 30431195 DOI: 10.1002/chem.201804505] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 10/26/2018] [Indexed: 12/19/2022]
Abstract
Precision glycomacromolecules have proven to be important tools for the investigation of multivalent carbohydrate-lectin interactions by presenting multiple glycan epitopes on a highly-defined synthetic scaffold. Herein, we present a new strategy for the versatile assembly of heteromultivalent glycomacromolecules that contain different carbohydrate motifs in proximity within the side chains. A new building block suitable for the solid-phase polymer synthesis of precision glycomacromolecules was developed with a branching point in the side chain that bears a free alkyne and a TIPS-protected alkyne moiety, which enables the subsequent attachment of different carbohydrate motifs by on-resin copper-mediated azide-alkyne cycloaddition reactions. Applying this synthetic strategy, heteromultivalent glycooligomers presenting fragments of histo-blood group antigens and human milk oligosaccharides were synthesized and tested for their binding behavior towards bacterial lectin LecB.
Collapse
Affiliation(s)
- Katharina S Bücher
- Institute of Organic and Macromolecular Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Patrick B Konietzny
- Institute of Organic and Macromolecular Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Nicole L Snyder
- Department of Chemistry, Davidson College, Davidson, NC, USA
| | - Laura Hartmann
- Institute of Organic and Macromolecular Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| |
Collapse
|
15
|
Sequence-to-structure dependence of isolated IgG Fc complex biantennaryN-glycans: a molecular dynamics study. Glycobiology 2018; 29:94-103. [DOI: 10.1093/glycob/cwy097] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 10/15/2018] [Indexed: 12/14/2022] Open
|
16
|
Tobola F, Lelimousin M, Varrot A, Gillon E, Darnhofer B, Blixt O, Birner-Gruenberger R, Imberty A, Wiltschi B. Effect of Noncanonical Amino Acids on Protein-Carbohydrate Interactions: Structure, Dynamics, and Carbohydrate Affinity of a Lectin Engineered with Fluorinated Tryptophan Analogs. ACS Chem Biol 2018; 13:2211-2219. [PMID: 29812892 PMCID: PMC6102642 DOI: 10.1021/acschembio.8b00377] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
Protein–carbohydrate
interactions play crucial roles in
biology. Understanding and modifying these interactions is of major
interest for fighting many diseases. We took a synthetic biology approach
and incorporated noncanonical amino acids into a bacterial lectin
to modulate its interactions with carbohydrates. We focused on tryptophan,
which is prevalent in carbohydrate binding sites. The exchange of
the tryptophan residues with analogs fluorinated at different positions
resulted in three distinctly fluorinated variants of the lectin from Ralstonia solanacearum. We observed differences in stability
and affinity toward fucosylated glycans and rationalized them by X-ray
and modeling studies. While fluorination decreased the aromaticity
of the indole ring and, therefore, the strength of carbohydrate–aromatic
interactions, additional weak hydrogen bonds were formed between fluorine
and the ligand hydroxyl groups. Our approach opens new possibilities
to engineer carbohydrate receptors.
Collapse
Affiliation(s)
- Felix Tobola
- Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria
| | | | | | - Emilie Gillon
- Univ. Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France
| | - Barbara Darnhofer
- Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria
- Research Unit of Functional Proteomics and Metabolomics, Institute of Pathology, Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria
- Omics Center Graz, BioTechMed-Graz, Stiftingtalstrasse 24, 8010 Graz, Austria
| | - Ola Blixt
- Department of Chemistry, Chemical Biology, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Ruth Birner-Gruenberger
- Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria
- Research Unit of Functional Proteomics and Metabolomics, Institute of Pathology, Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria
- Omics Center Graz, BioTechMed-Graz, Stiftingtalstrasse 24, 8010 Graz, Austria
| | - Anne Imberty
- Univ. Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France
| | - Birgit Wiltschi
- Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria
| |
Collapse
|
17
|
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.
Collapse
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
| |
Collapse
|
18
|
Taube S, Mallagaray A, Peters T. Norovirus, glycans and attachment. Curr Opin Virol 2018; 31:33-42. [DOI: 10.1016/j.coviro.2018.04.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 04/23/2018] [Accepted: 04/26/2018] [Indexed: 10/16/2022]
|
19
|
Alibay I, Burusco KK, Bruce NJ, Bryce RA. Identification of Rare Lewis Oligosaccharide Conformers in Aqueous Solution Using Enhanced Sampling Molecular Dynamics. J Phys Chem B 2018; 122:2462-2474. [PMID: 29419301 DOI: 10.1021/acs.jpcb.7b09841] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Determining the conformations accessible to carbohydrate ligands in aqueous solution is important for understanding their biological action. In this work, we evaluate the conformational free-energy surfaces of Lewis oligosaccharides in explicit aqueous solvent using a multidimensional variant of the swarm-enhanced sampling molecular dynamics (msesMD) method; we compare with multi-microsecond unbiased MD simulations, umbrella sampling, and accelerated MD approaches. For the sialyl Lewis A tetrasaccharide, msesMD simulations in aqueous solution predict conformer landscapes in general agreement with the other biased methods and with triplicate unbiased 10 μs trajectories; these simulations find a predominance of closed conformer and a range of low-occupancy open forms. The msesMD simulations also suggest closed-to-open transitions in the tetrasaccharide are facilitated by changes in ring puckering of its GlcNAc residue away from the 4C1 form, in line with previous work. For sialyl Lewis X tetrasaccharide, msesMD simulations predict a minor population of an open form in solution corresponding to a rare lectin-bound pose observed crystallographically. Overall, from comparison with biased MD calculations, we find that triplicate 10 μs unbiased MD simulations may not be enough to fully sample glycan conformations in aqueous solution. However, the computational efficiency and intuitive approach of the msesMD method suggest potential for its application in glycomics as a tool for analysis of oligosaccharide conformation.
Collapse
Affiliation(s)
- Irfan Alibay
- Division of Pharmacy and Optometry, School of Health Sciences, Manchester Academic Health Sciences Centre , University of Manchester , Oxford Road , Manchester M13 9PL , U.K
| | - Kepa K Burusco
- Division of Pharmacy and Optometry, School of Health Sciences, Manchester Academic Health Sciences Centre , University of Manchester , Oxford Road , Manchester M13 9PL , U.K
| | - Neil J Bruce
- Heidelberg Institute for Theoretical Studies , Schloss-Wolfsbrunnenweg 35 , Heidelberg 69118 , Germany
| | - Richard A Bryce
- Division of Pharmacy and Optometry, School of Health Sciences, Manchester Academic Health Sciences Centre , University of Manchester , Oxford Road , Manchester M13 9PL , U.K
| |
Collapse
|
20
|
Plazinski W, Plazinska A. Molecular dynamics simulations of hexopyranose ring distortion in different force fields. PURE APPL CHEM 2017. [DOI: 10.1515/pac-2016-0922] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract:The four classical, biomolecular force fields designed to study hexopyranose-based carbohydrates (GROMOS 56a6CARBO/56a6CARBO_R, GROMOS 53a6GLYC, CHARMM and GLYCAM06) have been tested in the context of ring-inversion properties. These properties were evaluated for both unfunctionalized monomers of all hexopyranoses of the d series and for residues in a chain composed of uniform units connected by α(1→4) and β(1→4) glycosidic linkages. The results indicate that the tested force fields differ in their predictions of the ring-inversion properties of both monomers and residues in a chain. The comparison with the available experimental data and with the semi-empirical Angyal scheme reveals that, at the level of monomers, GROMOS 56a6CARBO, GROMOS 53a6GLYC and CHARMM correctly reproduce the ring-inversion free energies. However, due to the lack of analogous reference data we cannot state which force field is more or less accurate in the context of ring distortion of residues in a chain. Therefore, the use of ab initio potentials is recommended in the prospective, quantitative studies on the related subject.
Collapse
Affiliation(s)
- Wojciech Plazinski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, ul. Niezapominajek 8, 30-239 Cracow, Poland, Tel.: +48815375685, Fax: +48815375685, e-mail:
| | - Anita Plazinska
- Department of Biopharmacy, Faculty of Pharmacy, Medical University of Lublin, W. Chodzki Str., 4a, 20-093 Lublin, Poland
| |
Collapse
|
21
|
Aeschbacher T, Zierke M, Smieško M, Collot M, Mallet JM, Ernst B, Allain FHT, Schubert M. A Secondary Structural Element in a Wide Range of Fucosylated Glycoepitopes. Chemistry 2017; 23:11598-11610. [PMID: 28654715 DOI: 10.1002/chem.201701866] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Indexed: 01/12/2023]
Abstract
The increasing understanding of the essential role of carbohydrates in development, and in a wide range of diseases fuels a rapidly growing interest in the basic principles governing carbohydrate-protein interactions. A still heavily debated issue regarding the recognition process is the degree of flexibility or rigidity of oligosaccharides. Combining NMR structure determination based on extensive experimental data with DFT and database searches, we have identified a set of trisaccharide motifs with a similar conformation that is characterized by a non-conventional C-H⋅⋅⋅O hydrogen bond. These motifs are present in numerous classes of oligosaccharides, found in everything from bacteria to mammals, including Lewis blood group antigens but also unusual motifs from amphibians and marine invertebrates. The set of trisaccharide motifs can be summarized with the consensus motifs X-β1,4-[Fucα1,3]-Y and X-β1,3-[Fucα1,4]-Y-a secondary structure we name [3,4]F-branch. The wide spectrum of possible modifications of this scaffold points toward a large variety of glycoepitopes, which nature generated using the same underlying architecture.
Collapse
Affiliation(s)
- Thomas Aeschbacher
- Institute of Molecular Biology and Biophysics, ETH Zürich, 8093, Zurich, Switzerland
| | - Mirko Zierke
- Institute of Molecular Pharmacy, University of Basel, Klingelbergstr. 50, 4056, Basel, Switzerland.,Department of Chemistry, University of British Columbia, V6T 1Z1, Vancouver, British Columbia, Canada
| | - Martin Smieško
- Institute of Molecular Pharmacy, University of Basel, Klingelbergstr. 50, 4056, Basel, Switzerland
| | - Mayeul Collot
- Laboratoire des Biomolécules, Département de Chimie, École normale supérieure, PSL Research University, Sorbonne Universités, UPMC Univ. Paris 06, CNRS, 24 rue Lhomond, 75005, Paris, France.,UMR 7213 CNRS, Laboratoire de Biophotonique et Pharmacologie, Faculté de Pharmacie, 74 route du Rhin, CS 60024, 67401, Illkirch, France
| | - Jean-Maurice Mallet
- Laboratoire des Biomolécules, Département de Chimie, École normale supérieure, PSL Research University, Sorbonne Universités, UPMC Univ. Paris 06, CNRS, 24 rue Lhomond, 75005, Paris, France
| | - Beat Ernst
- Institute of Molecular Pharmacy, University of Basel, Klingelbergstr. 50, 4056, Basel, Switzerland
| | - Frédéric H-T Allain
- Institute of Molecular Biology and Biophysics, ETH Zürich, 8093, Zurich, Switzerland
| | - Mario Schubert
- Institute of Molecular Biology and Biophysics, ETH Zürich, 8093, Zurich, Switzerland.,Institute of Molecular Biology, University of Salzburg, Billrothstr. 11, 5020, Salzburg, Austria
| |
Collapse
|
22
|
Bleuler-Martinez S, Stutz K, Sieber R, Collot M, Mallet JM, Hengartner M, Schubert M, Varrot A, Künzler M. Dimerization of the fungal defense lectin CCL2 is essential for its toxicity against nematodes. Glycobiology 2017; 27:486-500. [PMID: 27980000 DOI: 10.1093/glycob/cww113] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 11/09/2016] [Indexed: 11/12/2022] Open
Abstract
Lectins are used as defense effector proteins against predators, parasites and pathogens by animal, plant and fungal innate defense systems. These proteins bind to specific glycoepitopes on the cell surfaces and thereby interfere with the proper cellular functions of the various antagonists. The exact cellular toxicity mechanism is in many cases unclear. Lectin CCL2 of the mushroom Coprinopsis cinerea was previously shown to be toxic for Caenorhabditis elegans and Drosophila melanogaster. This toxicity is dependent on a single, high-affinity binding site for the trisaccharide GlcNAc(Fucα1,3)β1,4GlcNAc, which is a hallmark of nematode and insect N-glycan cores. The carbohydrate-binding site is located at an unusual position on the protein surface when compared to other β-trefoil lectins. Here, we show that CCL2 forms a compact dimer in solution and in crystals. Substitution of two amino acid residues at the dimer interface, R18A and F133A, interfered with dimerization of CCL2 and reduced toxicity but left carbohydrate-binding unaffected. These results, together with the positioning of the two carbohydrate-binding sites on the surface of the protein dimer, suggest that crosslinking of N-glycoproteins on the surface of intestinal cells of invertebrates is a crucial step in the mechanism of CCL2-mediated toxicity. Comparisons of the number and positioning of carbohydrate-binding sites among different dimerizing fungal β-trefoil lectins revealed a considerable variability in the carbohydrate-binding patterns of these proteins, which are likely to correlate with their respective functions.
Collapse
Affiliation(s)
| | - Katrin Stutz
- Institute of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Ramon Sieber
- Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Mayeul Collot
- Laboratoire des Biomolécules, UPMC Université Paris 06, Ecole Normale Supérieure, Paris, France
| | - Jean-Maurice Mallet
- Laboratoire des Biomolécules, UPMC Université Paris 06, Ecole Normale Supérieure, Paris, France
| | - Michael Hengartner
- Institute of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Mario Schubert
- Institute of Molecular Biology and Biophysics, ETH Zürich, Schafmattstr. 20, 8093 Zürich, Switzerland.,Department of Molecular Biology, University of Salzburg, Billrothstrasse 11, 5020 Salzburg, Austria
| | - Annabelle Varrot
- CERMAV, UPR5301, CNRS and Université Grenoble Alpes, 38041 Grenoble, France
| | - Markus Künzler
- Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| |
Collapse
|
23
|
Dingjan T, Imberty A, Pérez S, Yuriev E, Ramsland PA. Molecular Simulations of Carbohydrates with a Fucose-Binding Burkholderia ambifaria Lectin Suggest Modulation by Surface Residues Outside the Fucose-Binding Pocket. Front Pharmacol 2017; 8:393. [PMID: 28680402 PMCID: PMC5478714 DOI: 10.3389/fphar.2017.00393] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Accepted: 06/06/2017] [Indexed: 12/22/2022] Open
Abstract
Burkholderia ambifaria is an opportunistic respiratory pathogen belonging to the Burkholderia cepacia complex, a collection of species responsible for the rapidly fatal cepacia syndrome in cystic fibrosis patients. A fucose-binding lectin identified in the B. ambifaria genome, BambL, is able to adhere to lung tissue, and may play a role in respiratory infection. X-ray crystallography has revealed the bound complex structures for four fucosylated human blood group epitopes (blood group B, H type 1, H type 2, and Lex determinants). The present study employed computational approaches, including docking and molecular dynamics (MD), to extend the structural analysis of BambL-oligosaccharide complexes to include four additional blood group saccharides (A, Lea, Leb, and Ley) and a library of blood-group-related carbohydrates. Carbohydrate recognition is dominated by interactions with fucose via a hydrogen-bonding network involving Arg15, Glu26, Ala38, and Trp79 and a stacking interaction with Trp74. Additional hydrogen bonds to non-fucose residues are formed with Asp30, Tyr35, Thr36, and Trp74. BambL recognition is dominated by interactions with fucose, but also features interactions with other parts of the ligands that may modulate specificity or affinity. The detailed computational characterization of the BambL carbohydrate-binding site provides guidelines for the future design of lectin inhibitors.
Collapse
Affiliation(s)
- Tamir Dingjan
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash UniversityMelbourne, VIC, Australia
| | - Anne Imberty
- Centre de Recherches sur les Macromolécules Végétales, Centre National de la Recherche Scientifique UPR5301, Université Grenoble AlpesGrenoble, France
| | - Serge Pérez
- Département de Pharmacochimie Moléculaire, Centre National de la Recherche Scientifique, UMR5063, Université Grenoble AlpesGrenoble, France
| | - Elizabeth Yuriev
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash UniversityMelbourne, VIC, Australia
| | - Paul A Ramsland
- School of Science, RMIT UniversityMelbourne, VIC, Australia.,Department of Surgery Austin Health, University of MelbourneMelbourne, VIC, Australia.,Department of Immunology, Central Clinical School, Monash UniversityMelbourne, VIC, Australia.,Burnet InstituteMelbourne, VIC, Australia
| |
Collapse
|
24
|
Heggelund JE, Varrot A, Imberty A, Krengel U. Histo-blood group antigens as mediators of infections. Curr Opin Struct Biol 2017; 44:190-200. [PMID: 28544984 DOI: 10.1016/j.sbi.2017.04.001] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 04/04/2017] [Accepted: 04/05/2017] [Indexed: 01/07/2023]
Abstract
The critical first step of a microbial infection is usually the attachment of pathogens to host cell glycans. Targets on host tissues are in particular the histo-blood group antigens (HBGAs), which are present in rich diversity in the mucus layer and on the underlying mucosa. Recent structural and functional studies have revealed significant new insight into the molecular mechanisms, explaining why individuals with certain blood groups are at increased risk of some infections. The most prominent example of blood-group-associated diseases is cholera, caused by infection with Vibrio cholerae. Many other microbial pathogens, for example Pseudomonas aeruginosa infecting the airways, and enterotoxigenic Escherichia coli (ETEC) causing traveler's diarrhea, also bind to histo-blood group antigens, but show a less clear correlation with blood group phenotype. Yet other pathogens, for example norovirus and Helicobacter pylori, recognize HBGAs differently depending on the strain. In all cases, milk oligosaccharides can aid the hosts' defenses, acting as natural receptor decoys, and anti-infectious therapy can be designed along similar strategies. In this review, we focus on important infections of humans, but the molecular mechanisms are of general relevance to a broad range of microbial infections of humans and animals.
Collapse
Affiliation(s)
- Julie E Heggelund
- Department of Chemistry, University of Oslo, P.O. Box 1033, NO-0315 Blindern, Norway
| | - Annabelle Varrot
- Centre de Recherches sur les Macromolécules Végétales (CERMAV), CNRS and Université Grenoble Alpes, 38000 Grenoble, France
| | - Anne Imberty
- Centre de Recherches sur les Macromolécules Végétales (CERMAV), CNRS and Université Grenoble Alpes, 38000 Grenoble, France
| | - Ute Krengel
- Department of Chemistry, University of Oslo, P.O. Box 1033, NO-0315 Blindern, Norway.
| |
Collapse
|
25
|
Teaming up synthetic chemistry and histochemistry for activity screening in galectin-directed inhibitor design. Histochem Cell Biol 2016; 147:285-301. [PMID: 28013366 DOI: 10.1007/s00418-016-1525-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/23/2016] [Indexed: 01/08/2023]
Abstract
A hallmark of endogenous lectins is their ability to select a few distinct glycoconjugates as counterreceptors for functional pairing from the natural abundance of cellular glycoproteins and glycolipids. As a consequence, assays to assess inhibition of lectin binding should necessarily come as close as possible to the physiological situation, to characterize an impact of a synthetic compound on biorelevant binding with pharmaceutical perspective. We here introduce in a proof-of-principle manner work with sections of paraffin-embedded tissue (jejunum, epididymis) and labeled adhesion/growth-regulatory galectins, harboring one (galectin-1 and galectin-3) or two (galectin-8) types of lectin domain. Six pairs of synthetic lactosides from tailoring of the headgroup (3'-O-sulfation) and the aglycone (β-methyl to aromatic S- and O-linked extensions) as well as three bi- to tetravalent glycoclusters were used as test compounds. Varying extents of reduction in staining intensity by synthetic compounds relative to unsubstituted/free lactose proved the applicability and sensitivity of the method. Flanking cytofluorimetric assays on lectin binding to native cells gave similar grading, excluding a major impact of tissue fixation. The experiments revealed cell/tissue binding of galectin-8 preferentially via one domain, depending on the cell type so that the effect of an inhibitor in a certain context cannot be extrapolated to other cells/tissues. Moreover, the work with the other galectins attests that this assay enables comprehensive analysis of the galectin network in serial tissue sections to determine overlaps and regional differences in inhibitory profiles.
Collapse
|
26
|
Agirre J, Davies GJ, Wilson KS, Cowtan KD. Carbohydrate structure: the rocky road to automation. Curr Opin Struct Biol 2016; 44:39-47. [PMID: 27940408 DOI: 10.1016/j.sbi.2016.11.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 10/26/2016] [Accepted: 11/10/2016] [Indexed: 11/29/2022]
Abstract
With the introduction of intuitive graphical software, structural biologists who are not experts in crystallography are now able to build complete protein or nucleic acid models rapidly. In contrast, carbohydrates are in a wholly different situation: scant automation exists, with manual building attempts being sometimes toppled by incorrect dictionaries or refinement problems. Sugars are the most stereochemically complex family of biomolecules and, as pyranose rings, have clear conformational preferences. Despite this, all refinement programs may produce high-energy conformations at medium to low resolution, without any support from the electron density. This problem renders the affected structures unusable in glyco-chemical terms. Bringing structural glycobiology up to 'protein standards' will require a total overhaul of the methodology. Time is of the essence, as the community is steadily increasing the production rate of glycoproteins, and electron cryo-microscopy has just started to image them in precisely that resolution range where crystallographic methods falter most.
Collapse
Affiliation(s)
- Jon Agirre
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK.
| | - Gideon J Davies
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Keith S Wilson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Kevin D Cowtan
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK.
| |
Collapse
|
27
|
Antibody recognition of aberrant glycosylation on the surface of cancer cells. Curr Opin Struct Biol 2016; 44:1-8. [PMID: 27821276 DOI: 10.1016/j.sbi.2016.10.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 09/28/2016] [Accepted: 10/13/2016] [Indexed: 11/23/2022]
Abstract
Carbohydrate-binding antibodies and carbohydrate-based vaccines are being actively pursued as targeted immunotherapies for a broad range of cancers. Recognition of tumor-associated carbohydrates (glycans) by antibodies is predominantly towards terminal epitopes on glycoproteins and glycolipids on the surface of cancer cells. Crystallography along with complementary experimental and computational methods have been extensively used to dissect antibody recognition of glycan epitopes commonly found in cancer. We provide an overview of the structural biology of antibody recognition of tumor-associated glycans and propose potential rearrangements of these targets in the membrane that could dictate the complex biological activities of these antibodies against cancer cells.
Collapse
|
28
|
Joosten RP, Lütteke T. Carbohydrate 3D structure validation. Curr Opin Struct Biol 2016; 44:9-17. [PMID: 27816840 DOI: 10.1016/j.sbi.2016.10.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 10/07/2016] [Accepted: 10/13/2016] [Indexed: 12/11/2022]
Abstract
Glycoproteins and protein-carbohydrate complexes in the worldwide Protein Data Bank (wwPDB) can be an excellent source of information for glycoscientists. Unfortunately, a rather large number of errors and inconsistencies is found in the glycan moieties of these 3D structures. This review illustrates frequent problems of carbohydrate moieties in wwPDB entries, such as nomenclature issues, incorrect N-glycan core structures, missing or erroneous linkages, or poor glycan geometry, and describes the carbohydrate-specific validation tools that are designed to identify such problems. Recommendations how to avoid these issues or how to rectify incorrect structures are also given.
Collapse
Affiliation(s)
- Robbie P Joosten
- Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Thomas Lütteke
- Institute of Veterinary Physiology and Biochemistry, Justus-Liebig-University Giessen, Frankfurter Str. 100, 35392 Giessen, Germany.
| |
Collapse
|