1
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Murphy PV, Dhara A, Fitzgerald LS, Hever E, Konda S, Mandal K. Small lectin ligands as a basis for applications in glycoscience and glycomedicine. Chem Soc Rev 2024; 53:9428-9445. [PMID: 39162695 DOI: 10.1039/d4cs00642a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/21/2024]
Abstract
Glycan recognition by lectins mediates important biological events. This Tutorial Review aims to introduce lectin-ligand interactions and show how these molecular recognition events inspire innovations such as: (i) glycomimetic ligands; (ii) multivalent ligand agonists/antagonists; (iii) ligands for precision delivery of therapies to cells, where therapies include vaccines, siRNA and LYTACs (iv) development of diagnostics. A small number of case studies are selected to demonstrate principles for development of new ligands for applications inspired by knowledge of natural glycan ligand structure and function.
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Affiliation(s)
- Paul V Murphy
- School of Biological and Chemical Sciences, Galway, H91TK33, Ireland.
- SSPC, SFI Research Centre for Pharmaceuticals, Galway, H91TK33, Ireland
- CÚRAM, SFI Research Centre for Medical Devices, University of Galway, University Road, Galway, H91TK33, Ireland
| | - Ashis Dhara
- School of Biological and Chemical Sciences, Galway, H91TK33, Ireland.
- SSPC, SFI Research Centre for Pharmaceuticals, Galway, H91TK33, Ireland
| | - Liam S Fitzgerald
- School of Biological and Chemical Sciences, Galway, H91TK33, Ireland.
- SSPC, SFI Research Centre for Pharmaceuticals, Galway, H91TK33, Ireland
- CÚRAM, SFI Research Centre for Medical Devices, University of Galway, University Road, Galway, H91TK33, Ireland
| | - Eoin Hever
- School of Biological and Chemical Sciences, Galway, H91TK33, Ireland.
| | - Saidulu Konda
- School of Biological and Chemical Sciences, Galway, H91TK33, Ireland.
| | - Kishan Mandal
- School of Biological and Chemical Sciences, Galway, H91TK33, Ireland.
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2
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Hewson AR, Lloyd-Laney HO, Keenan T, Richards SJ, Gibson MI, Linclau B, Signoret N, Fascione MA, Parkin A. Harnessing glycofluoroforms for impedimetric biosensing. Chem Sci 2024:d4sc04409f. [PMID: 39282644 PMCID: PMC11393611 DOI: 10.1039/d4sc04409f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Accepted: 09/04/2024] [Indexed: 09/19/2024] Open
Abstract
Glycans play a major role in biological cell-cell recognition and signal transduction but have found limited application in biosensors due to glycan/lectin promiscuity; multiple proteins are capable of binding to the same native glycan. Here, site-specific fluorination is used to introduce protein-glycan selectivity, and this is coupled with an electrochemical detection method to generate a novel biosensor platform. 3F-lacto-N-biose glycofluoroform is installed onto polymer tethers, which are subsequently immobilised onto gold screen printed electrodes, providing a non-fouling surface. The impedance biosensing platform is shown to selectively bind cancer-associated galectin-3 compared to control glycans and proteins. To improve the analytical capability, Bayesian statistical analysis was deployed in the equivalent circuit fitting of electrochemical impedance spectroscopy data. It is shown that Markov Chain Monte Carlo (MCMC) analysis is a helpful method for visualising experimental irreproducibility, and we apply this as a quality control step.
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Affiliation(s)
- Alice R Hewson
- Department of Chemistry, University of York YO10 5DD York UK
| | | | - Tessa Keenan
- Department of Chemistry, University of York YO10 5DD York UK
| | - Sarah-Jane Richards
- Department of Chemistry, The University of Manchester M13 9PL UK
- Manchester Institute of Biotechnology, The University of Manchester M1 7DN UK
| | - Matthew I Gibson
- Department of Chemistry, The University of Manchester M13 9PL UK
- Manchester Institute of Biotechnology, The University of Manchester M1 7DN UK
| | - Bruno Linclau
- Department of Organic and Macromolecular Chemistry, Ghent University Krijgslaan 281-S4 9000 Gent Belgium
- School of Chemistry, University of Southampton Highfield Southampton SO17 1BJ UK
| | | | | | - Alison Parkin
- Department of Chemistry, University of York YO10 5DD York UK
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3
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Hollingsworth K, Di Maio A, Richards SJ, Vendeville JB, Wheatley DE, Council CE, Keenan T, Ledru H, Chidwick H, Huang K, Parmeggiani F, Marchesi A, Chai W, McBerney R, Kamiński TP, Balmforth MR, Tamasanu A, Finnigan JD, Young C, Warriner SL, Webb ME, Fascione MA, Flitsch S, Galan MC, Feizi T, Gibson MI, Liu Y, Turnbull WB, Linclau B. Synthesis and screening of a library of Lewis x deoxyfluoro-analogues reveals differential recognition by glycan-binding partners. Nat Commun 2024; 15:7925. [PMID: 39271664 PMCID: PMC11399408 DOI: 10.1038/s41467-024-51081-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 07/30/2024] [Indexed: 09/15/2024] Open
Abstract
Glycan-mediated interactions play a crucial role in biology and medicine, influencing signalling, immune responses, and disease pathogenesis. However, the use of glycans in biosensing and diagnostics is limited by cross-reactivity, as certain glycan motifs can be recognised by multiple biologically distinct protein receptors. To address this specificity challenge, we report the enzymatic synthesis of a 150-member library of site-specifically fluorinated Lewisx analogues ('glycofluoroforms') using naturally occurring enzymes and fluorinated monosaccharides. Subsequent incorporation of a subset of these glycans into nanoparticles or a microarray revealed a striking spectrum of distinct binding intensities across different proteins that recognise Lewisx. Notably, we show that for two proteins with unique binding sites for Lewisx, glycofluoroforms exhibited enhanced binding to one protein, whilst reduced binding to the other, with selectivity governed by fluorination patterns. We finally showcase the potential diagnostic utility of this approach in glycofluoroform-mediated bacterial toxin detection by lateral flow.
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Affiliation(s)
- Kristian Hollingsworth
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Antonio Di Maio
- Glycosciences Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Sarah-Jane Richards
- Department of Chemistry, University of Warwick, Coventry, UK
- Manchester Institute of Biotechnology (MIB), Department of Chemistry, University of Manchester, Manchester, UK
| | | | - David E Wheatley
- School of Chemistry, University of Southampton, Highfield, Southampton, UK
| | - Claire E Council
- School of Chemistry, University of Southampton, Highfield, Southampton, UK
| | - Tessa Keenan
- Department of Chemistry, University of York, Heslington, York, UK
| | - Hélène Ledru
- School of Chemistry, Cantock's Close, University of Bristol, Bristol, UK
| | - Harriet Chidwick
- Department of Chemistry, University of York, Heslington, York, UK
| | - Kun Huang
- Manchester Institute of Biotechnology (MIB), Department of Chemistry, University of Manchester, Manchester, UK
| | - Fabio Parmeggiani
- Manchester Institute of Biotechnology (MIB), Department of Chemistry, University of Manchester, Manchester, UK
| | - Andrea Marchesi
- Manchester Institute of Biotechnology (MIB), Department of Chemistry, University of Manchester, Manchester, UK
| | - Wengang Chai
- Glycosciences Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Ryan McBerney
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Tomasz P Kamiński
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Matthew R Balmforth
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Alexandra Tamasanu
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - James D Finnigan
- Prozomix Limited, Haltwhistle Industrial Estate, Haltwhistle, Northumberland, UK
| | - Carl Young
- Prozomix Limited, Haltwhistle Industrial Estate, Haltwhistle, Northumberland, UK
| | - Stuart L Warriner
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Michael E Webb
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | | | - Sabine Flitsch
- Manchester Institute of Biotechnology (MIB), Department of Chemistry, University of Manchester, Manchester, UK
| | - M Carmen Galan
- School of Chemistry, Cantock's Close, University of Bristol, Bristol, UK
| | - Ten Feizi
- Glycosciences Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.
| | - Matthew I Gibson
- Department of Chemistry, University of Warwick, Coventry, UK.
- Manchester Institute of Biotechnology (MIB), Department of Chemistry, University of Manchester, Manchester, UK.
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK.
| | - Yan Liu
- Glycosciences Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.
| | - W Bruce Turnbull
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK.
| | - Bruno Linclau
- School of Chemistry, University of Southampton, Highfield, Southampton, UK.
- Department of Organic and Macromolecular Chemistry, Ghent University, Ghent, Belgium.
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4
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Kurfiřt M, Št'astná LČ, Dračínský M, Pohl R, Císařová I, Sýkora J, Balouch M, Baka M, Hamala V, Cañada FJ, Ardá A, Jiménez-Barbero J, Karban J. Influence of Selective Deoxyfluorination on the Molecular Structure of Type-2 N-Acetyllactosamine. J Org Chem 2024; 89:11875-11890. [PMID: 39178339 PMCID: PMC11382267 DOI: 10.1021/acs.joc.4c00879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/25/2024]
Abstract
N-Acetyllactosamine is a common saccharide motif found in various biologically active glycans. This motif usually works as a backbone for additional modifications and thus significantly influences glycan conformational behavior and biological activity. In this work, we have investigated the type-2 N-acetyllactosamine scaffold using the complete series of its monodeoxyfluorinated analogs. These glycomimetics have been studied by molecular mechanics, quantum mechanics, X-ray crystallography, and various NMR techniques, which have provided a comprehensive and complete insight into the role of individual hydroxyl groups in the conformational behavior and lipophilicity of N-acetyllactosamine.
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Affiliation(s)
- Martin Kurfiřt
- Institute of Chemical Process Fundamentals, Czech Academy of Sciences, Rozvojová 1/135, CZ-165 00 Praha 6, Czech Republic
| | - Lucie Červenková Št'astná
- Institute of Chemical Process Fundamentals, Czech Academy of Sciences, Rozvojová 1/135, CZ-165 00 Praha 6, Czech Republic
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 542/2, CZ-160 00 Praha 6, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 542/2, CZ-160 00 Praha 6, Czech Republic
| | - Ivana Císařová
- Department of Inorganic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-128 43 Praha 2, Czech Republic
| | | | | | - Michal Baka
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Vojtěch Hamala
- Institute of Chemical Process Fundamentals, Czech Academy of Sciences, Rozvojová 1/135, CZ-165 00 Praha 6, Czech Republic
| | - F Javier Cañada
- Centro de Investigaciones Biológicas Margarita Salas, Ramiro de Maeztu 9, 28040 Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Avda Monforte de Lemos 3-5, 28029 Madrid, Spain
| | - Ana Ardá
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48162 Derio Bizkaia, Spain
- Ikerbasque, Basque Foundation for Science, Plaza Euskadi 2, 48013 Bilbao Bizkaia, Spain
| | - Jesús Jiménez-Barbero
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48162 Derio Bizkaia, Spain
- Ikerbasque, Basque Foundation for Science, Plaza Euskadi 2, 48013 Bilbao Bizkaia, Spain
- Department of Organic and Inorganic Chemistry, Faculty of Science and Technology, University of the Basque Country, EHU-UPV, 48940 Leioa, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Avda Monforte de Lemos 3-5, 28029 Madrid, Spain
| | - Jindřich Karban
- Institute of Chemical Process Fundamentals, Czech Academy of Sciences, Rozvojová 1/135, CZ-165 00 Praha 6, Czech Republic
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5
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Nieto-Fabregat F, Lenza MP, Marseglia A, Di Carluccio C, Molinaro A, Silipo A, Marchetti R. Computational toolbox for the analysis of protein-glycan interactions. Beilstein J Org Chem 2024; 20:2084-2107. [PMID: 39189002 PMCID: PMC11346309 DOI: 10.3762/bjoc.20.180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 08/01/2024] [Indexed: 08/28/2024] Open
Abstract
Protein-glycan interactions play pivotal roles in numerous biological processes, ranging from cellular recognition to immune response modulation. Understanding the intricate details of these interactions is crucial for deciphering the molecular mechanisms underlying various physiological and pathological conditions. Computational techniques have emerged as powerful tools that can help in drawing, building and visualising complex biomolecules and provide insights into their dynamic behaviour at atomic and molecular levels. This review provides an overview of the main computational tools useful for studying biomolecular systems, particularly glycans, both in free state and in complex with proteins, also with reference to the principles, methodologies, and applications of all-atom molecular dynamics simulations. Herein, we focused on the programs that are generally employed for preparing protein and glycan input files to execute molecular dynamics simulations and analyse the corresponding results. The presented computational toolbox represents a valuable resource for researchers studying protein-glycan interactions and incorporates advanced computational methods for building, visualising and predicting protein/glycan structures, modelling protein-ligand complexes, and analyse MD outcomes. Moreover, selected case studies have been reported to highlight the importance of computational tools in studying protein-glycan systems, revealing the capability of these tools to provide valuable insights into the binding kinetics, energetics, and structural determinants that govern specific molecular interactions.
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Affiliation(s)
- Ferran Nieto-Fabregat
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126, Italy
| | - Maria Pia Lenza
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126, Italy
| | - Angela Marseglia
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126, Italy
| | - Cristina Di Carluccio
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126, Italy
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126, Italy
| | - Alba Silipo
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126, Italy
| | - Roberta Marchetti
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126, Italy
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6
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Seibel J, Anggara K, Delbianco M, Rauschenbach S. Scanning Probe Microscopy Characterization of Biomolecules enabled by Mass-Selective, Soft-landing Electrospray Ion Beam Deposition. Chemphyschem 2024:e202400419. [PMID: 38945838 DOI: 10.1002/cphc.202400419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 07/02/2024]
Abstract
Scanning probe microscopy (SPM), in particular at low temperature (LT) under ultra-high vacuum (UHV) conditions, offers the possibility of real-space imaging with resolution reaching the atomic level. However, its potential for the analysis of complex biological molecules has been hampered by requirements imposed by sample preparation. Transferring molecules onto surfaces in UHV is typically accomplished by thermal sublimation in vacuum. This approach however is limited by the thermal stability of the molecules, i. e. not possible for biological molecules with low vapour pressure. Bypassing this limitation, electrospray ionisation offers an alternative method to transfer molecules from solution to the gas-phase as intact molecular ions. In soft-landing electrospray ion beam deposition (ESIBD), these molecular ions are subsequently mass-selected and gently landed on surfaces which permits large and thermally fragile molecules to be analyzed by LT-UHV SPM. In this concept, we discuss how ESIBD+SPM prepares samples of complex biological molecules at a surface, offering controls of the molecular structural integrity, three-dimensional shape, and purity. These achievements unlock the analytical potential of SPM which is showcased by imaging proteins, peptides, DNA, glycans, and conjugates of these molecules, revealing details of their connectivity, conformation, and interaction that could not be accessed by any other technique.
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Affiliation(s)
- Johannes Seibel
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Fritz-Haber Weg 2, D-76131, Karlsruhe, Germany
| | - Kelvin Anggara
- Nanoscale Science Department, Max Planck Institute for Solid State Research, Heisenbergstr. 1, D-70569, Stuttgart, Germany
| | - Martina Delbianco
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, D-14476, Potsdam, Germany
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7
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Wu Y, Tang C, Lee JT, Zhang R, Bhunia S, Kundu P, Stern CL, Chen AXY, Shen D, Yang S, Han H, Li X, Wu H, Feng Y, Armstrong DW, Stoddart JF. Metal-Assisted Carbohydrate Assembly. J Am Chem Soc 2024; 146:9801-9810. [PMID: 38551407 DOI: 10.1021/jacs.3c14427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
The sequence-controlled assembly of nucleic acids and amino acids into well-defined superstructures constitutes one of the most revolutionary technologies in modern science. The elaboration of such superstructures from carbohydrates, however, remains elusive and largely unexplored on account of their intrinsic constitutional and configurational complexity, not to mention their inherent conformational flexibility. Here, we report the bottom-up assembly of two classes of hierarchical superstructures that are formed from a highly flexible cyclo-oligosaccharide─namely, cyclofructan-6 (CF-6). The formation of coordinative bonds between the oxygen atoms of CF-6 and alkali metal cations (i) locks a myriad of flexible conformations of CF-6 into a few rigid conformations, (ii) bridges adjacent CF-6 ligands, and (iii) gives rise to the multiple-level assembly of three extended frameworks. The hierarchical superstructures present in these frameworks have been shown to modulate their nanomechanical properties. This research highlights the unique opportunities of constructing convoluted superstructures from carbohydrates and should encourage future endeavors in this underinvestigated field of science.
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Affiliation(s)
- Yong Wu
- Department of Chemistry, The University of Hong Kong, Hong Kong SAR 999077, China
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Chun Tang
- Department of Chemistry, The University of Hong Kong, Hong Kong SAR 999077, China
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | | | - Ruihua Zhang
- Department of Chemistry, The University of Hong Kong, Hong Kong SAR 999077, China
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Surojit Bhunia
- Department of Chemistry, The University of Hong Kong, Hong Kong SAR 999077, China
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Pramita Kundu
- Department of Chemistry, The University of Hong Kong, Hong Kong SAR 999077, China
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Charlotte L Stern
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Aspen X-Y Chen
- Department of Chemistry, The University of Hong Kong, Hong Kong SAR 999077, China
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Dengke Shen
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China
| | - Shuliang Yang
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Han Han
- Department of Chemistry, The University of Hong Kong, Hong Kong SAR 999077, China
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Xuesong Li
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- Department of Chemistry, University of Wyoming, Laramie, Wyoming 82072, United States
| | - Huang Wu
- Department of Chemistry, The University of Hong Kong, Hong Kong SAR 999077, China
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Yuanning Feng
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- Department of Chemistry and Biochemistry, The University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Daniel W Armstrong
- AZYP LLC, Arlington, Texas 76019, United States
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019, United States
| | - J Fraser Stoddart
- Department of Chemistry, The University of Hong Kong, Hong Kong SAR 999077, China
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, Illinois 60611, United States
- Stoddart Institute of Molecular Science, Department of Chemistry, Zhejiang University, Hangzhou, Zhejiang 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, Zhejiang 311215, China
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
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8
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Yadav N, Djalali S, Poveda A, Ricardo MG, Seeberger PH, Jiménez-Barbero J, Delbianco M. Dissecting the Conformational Stability of a Glycan Hairpin. J Am Chem Soc 2024; 146:6369-6376. [PMID: 38377472 PMCID: PMC10921397 DOI: 10.1021/jacs.4c00423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/07/2024] [Accepted: 02/12/2024] [Indexed: 02/22/2024]
Abstract
Systematic structural studies of model oligopeptides revealed important aspects of protein folding and offered design principles to access non-natural materials. In the same way, the rules that regulate glycan folding could be established by studying synthetic oligosaccharide models. However, their analysis is often limited due to the synthetic and analytical complexity. By utilizing a glycan capable of spontaneously folding into a hairpin conformation as a model system, we investigated the factors that contribute to its conformational stability in aqueous solution. The modular design of the hairpin model featured a trisaccharide turn unit and two β-1,4-oligoglucoside stacking strands that allowed for systematic chemical modifications of the glycan sequence, including the introduction of NMR labels and staples. Nuclear magnetic resonance assisted by molecular dynamics simulations revealed that stereoelectronic effects and multiple glycan-glycan interactions are the major determinants of folding stabilization. Chemical modifications in the glycan primary sequence (e.g., strand elongation) can be employed to fine-tune the rigidity of structural motifs distant from the modification sites. These results could inspire the design of other glycan architectures, with implications in glycobiology and material sciences.
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Affiliation(s)
- Nishu Yadav
- Department
of Biomolecular Systems, Max Planck Institute
of Colloids and Interfaces, Am Mühlenberg 1, Potsdam 14476, Germany
- Department
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, Berlin 14195, Germany
| | - Surusch Djalali
- Department
of Biomolecular Systems, Max Planck Institute
of Colloids and Interfaces, Am Mühlenberg 1, Potsdam 14476, Germany
- Department
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, Berlin 14195, Germany
| | - Ana Poveda
- CIC
bioGUNE, Basque Research and Technology Alliance, Derio 48160, Spain
| | - Manuel G. Ricardo
- Department
of Biomolecular Systems, Max Planck Institute
of Colloids and Interfaces, Am Mühlenberg 1, Potsdam 14476, Germany
| | - Peter H. Seeberger
- Department
of Biomolecular Systems, Max Planck Institute
of Colloids and Interfaces, Am Mühlenberg 1, Potsdam 14476, Germany
- Department
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, Berlin 14195, Germany
| | - Jesús Jiménez-Barbero
- CIC
bioGUNE, Basque Research and Technology Alliance, Derio 48160, Spain
- Ikerbasque,
Basque Foundation for Science, Bilbao 48009, Spain
- Department
of Inorganic & Organic Chemistry, Faculty of Science and Technology, University of the Basque Country, EHU-UPV, Leioa 48940, Spain
- Centro de
Investigación Biomedica en Red de Enfermedades Respiratorias, Madrid 28029, Spain
| | - Martina Delbianco
- Department
of Biomolecular Systems, Max Planck Institute
of Colloids and Interfaces, Am Mühlenberg 1, Potsdam 14476, Germany
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9
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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.
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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.
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10
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Dabravolski SA, Sukhorukov VN, Melnichenko AA, Khotina VA, Orekhov AN. Oligosaccharides as Potential Therapeutics against Atherosclerosis. Molecules 2023; 28:5452. [PMID: 37513323 PMCID: PMC10386248 DOI: 10.3390/molecules28145452] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Atherosclerosis is the major cause of cardiovascular-disease-related death worldwide, resulting from the subendothelial accumulation of lipoprotein-derived cholesterol, ultimately leading to chronic inflammation and the formation of clinically significant atherosclerotic plaques. Oligosaccharides have been widely used in biomedical research and therapy, including tissue engineering, wound healing, and drug delivery. Moreover, oligosaccharides have been consumed by humans for centuries, and are cheap, and available in large amounts. Given the constantly increasing number of obesity, diabetes, and hyperlipidaemia cases, there is an urgent need for novel therapeutics that can economically and effectively slow the progression of atherosclerosis. In this review, we address the current state of knowledge in oligosaccharides research, and provide an update of the recent in vitro and in vivo experiments that precede clinical studies. The application of oligosaccharides could help to eliminate the residual risk after the application of other cholesterol-lowering medicines, and provide new therapeutic opportunities to reduce the associated burden of premature deaths because of atherosclerosis.
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Affiliation(s)
- Siarhei A Dabravolski
- Department of Biotechnology Engineering, Braude Academic College of Engineering, Snunit 51, P.O. Box 78, Karmiel 2161002, Israel
| | - Vasily N Sukhorukov
- Institute of General Pathology and Pathophysiology, 8 Baltiyskaya Street, 125315 Moscow, Russia
| | - Alexandra A Melnichenko
- Institute of General Pathology and Pathophysiology, 8 Baltiyskaya Street, 125315 Moscow, Russia
| | - Victoria A Khotina
- Institute of General Pathology and Pathophysiology, 8 Baltiyskaya Street, 125315 Moscow, Russia
| | - Alexander N Orekhov
- Institute of General Pathology and Pathophysiology, 8 Baltiyskaya Street, 125315 Moscow, Russia
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11
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Stephens Z, Wilson LFL, Zimmer J. Diverse mechanisms of polysaccharide biosynthesis, assembly and secretion across kingdoms. Curr Opin Struct Biol 2023; 79:102564. [PMID: 36870276 DOI: 10.1016/j.sbi.2023.102564] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 01/16/2023] [Accepted: 01/28/2023] [Indexed: 03/06/2023]
Abstract
Polysaccharides are essential biopolymers produced in all kingdoms of life. On the cell surface, they represent versatile architectural components, forming protective capsules and coats, cell walls, or adhesives. Extracellular polysaccharide (EPS) biosynthesis mechanisms differ based on the cellular localization of polymer assembly. Some polysaccharides are first synthesized in the cytosol and then extruded by ATP powered transporters [1]. In other cases, the polymers are assembled outside the cell [2], synthesized and secreted in a single step [3], or deposited on the cell surface via vesicular trafficking [4]. This review focuses on recent insights into the biosynthesis, secretion, and assembly of EPS in microbes, plants and vertebrates. We focus on comparing the sites of biosynthesis, secretion mechanisms, and higher-order EPS assemblies.
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Affiliation(s)
- Zachery Stephens
- Howard Hughes Medical Institute, University of Virginia School of Medicine, Charlottesville, VA, USA; Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, 480 Ray C. Hunt Dr., Charlottesville, VA 22908, USA
| | - Louis F L Wilson
- Howard Hughes Medical Institute, University of Virginia School of Medicine, Charlottesville, VA, USA; Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, 480 Ray C. Hunt Dr., Charlottesville, VA 22908, USA
| | - Jochen Zimmer
- Howard Hughes Medical Institute, University of Virginia School of Medicine, Charlottesville, VA, USA; Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, 480 Ray C. Hunt Dr., Charlottesville, VA 22908, USA.
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12
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Interaction of Chondroitin and Hyaluronan Glycosaminoglycans with Surfaces of Carboxylated Carbon Nanotubes Studied Using Molecular Dynamics Simulations. MOLECULES (BASEL, SWITZERLAND) 2023; 28:molecules28020826. [PMID: 36677880 PMCID: PMC9861662 DOI: 10.3390/molecules28020826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/05/2023] [Accepted: 01/10/2023] [Indexed: 01/19/2023]
Abstract
Interaction of β-D-glucopyranuronic acid (GlcA), N-acetyl-β-D-glucosamine (GlcNAc), N-acetyl-β-D-galactosamine (GalNAc) and two natural decameric glycosaminoglycans, hyaluronic acid (HA) and Chondroitin (Ch) with carboxylated carbon nanotubes, were studied using molecular dynamics simulations in a condensed phase. The force field used for carbohydrates was the GLYCAM-06j version, while functionalized carbon nanotubes (fCNT) were described using version two of the general amber force field. We found a series of significant differences in carbohydrate-fCNT adsorption strength depending on the monosaccharide molecule and protonation state of surface carboxyl groups. GlcNAc and GalNAc reveal a strong adsorption on fCNT with deprotonated carboxyl groups, and a slightly weaker adsorption on the fCNT with protonated carboxyl groups. On the contrary, GlcA weakly adsorbs on fCNT. The change in protonation state of surface carboxyl groups leads to the reversal orientation of GlcNAc and GalNAc in reference to the fCNT surface, while GlcA is not sensitive to that factor. Adsorption of decameric oligomers on the surface of fCNT weakens with the increasing number of monosaccharide units. Chondroitin adsorbs weaker than hyaluronic acid and incorporation of four Ch molecules leads to partial detachment of them from the fCNT surface. The glycan-fCNT interactions are strong enough to alter the conformation of carbohydrate backbone; the corresponding conformational changes act toward a more intensive contact of glycan with the fCNT surface. Structural and energetic features of the adsorption process suggest the CH-π interaction-driven mechanism.
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13
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Dal Colle MCS, Fittolani G, Delbianco M. Synthetic Approaches to Break the Chemical Shift Degeneracy of Glycans. Chembiochem 2022; 23:e202200416. [PMID: 36005282 PMCID: PMC10087674 DOI: 10.1002/cbic.202200416] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/24/2022] [Indexed: 01/25/2023]
Abstract
NMR spectroscopy is the leading technique for determining glycans' three-dimensional structure and dynamic in solution as well as a fundamental tool to study protein-glycan interactions. To overcome the severe chemical shift degeneracy of these compounds, synthetic probes carrying NMR-active nuclei (e. g., 13 C or 19 F) or lanthanide tags have been proposed. These elegant strategies permitted to simplify the complex NMR analysis of unlabeled analogues, shining light on glycans' conformational aspects and interaction with proteins. Here, we highlight some key achievements in the synthesis of specifically labeled glycan probes and their contribution towards the fundamental understanding of glycans.
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Affiliation(s)
- Marlene C. S. Dal Colle
- Department of Biomolecular SystemsMax-Planck-Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
- Department of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
| | - Giulio Fittolani
- 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
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14
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Tetrault T, Meredith RJ, Zhang W, Carmichael I, Serianni AS. One-Bond 13C- 1H and 13C- 13C Spin-Coupling Constants as Constraints in MA'AT Analysis of Saccharide Conformation. J Phys Chem B 2022; 126:9506-9515. [PMID: 36356177 DOI: 10.1021/acs.jpcb.2c04986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
MA'AT analysis uses ensembles of redundant experimental NMR spin-coupling constants, parametrized J-coupling equations obtained from density functional theory (DFT) calculations, and circular statistics to produce probability distributions of molecular torsion angles in solution and information on librational motions about these angles (Meredith et al., J. Chem. Info. Model. 2022, 62, 3135-3141). Current DFT methods give nearly quantitative two- and three-bond JHH, JCH, and 1JCC values for use in MA'AT analysis of saccharides. In contrast, the accuracy of DFT-calculated one-bond 1JCH and 1JCC values is more difficult to determine, preventing their use in MA'AT modeling. This report describes experimental and computational studies that address this problem using two approaches (Strategies 1 and 2). Differences [1JCHcalc - 1JCHexp] (Strategy 1) ranged from -1.2 to 2.5 Hz, giving an average difference of 0.8 ± 1.7 Hz. Percent differences ranged from -0.8% to 1.6%, giving an average % difference of 0.5 ± 1.1%. In comparison, [1JCHMA'AT - 1JCHexp] (Strategy 2) ranged from -1.8 to 0.2 Hz, giving an average difference of -1.2 ± 0.7 Hz. Percent differences ranged from -1.2% to 0.1%, giving an average % difference of -0.8 ± 0.5%. Strategy 1 gave an average difference of 2.1 Hz between calculated and experimental 1JCC values, with an average % difference of 5.1 ± 0.2%. Calculated 1JCC values were consistently larger than experimental values. Strategy 2 also gave calculated 1JCC values that were larger than the experimental values, with an average difference of 2.3 ± 0.6 Hz, and an average % difference of 5.6 ± 1.6%. The findings of both strategies are similar and indicate that 1JCH values in saccharides can be calculated nearly quantitatively, but 1JCC values appear to be consistently overestimated by ∼5% using current DFT methods.
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Affiliation(s)
| | | | - Wenhui Zhang
- Omicron Biochemicals, Inc., South Bend, Indiana 46617, United States
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15
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Abstract
Fluorinated carbohydrates have found many applications in the glycosciences. Typically, these contain fluorination at a single position. There are not many applications involving polyfluorinated carbohydrates, here defined as monosaccharides in which more than one carbon has at least one fluorine substituent directly attached to it, with the notable exception of their use as mechanism-based inhibitors. The increasing attention to carbohydrate physical properties, especially around lipophilicity, has resulted in a surge of interest for this class of compounds. This review covers the considerable body of work toward the synthesis of polyfluorinated hexoses, pentoses, ketosugars, and aminosugars including sialic acids and nucleosides. An overview of the current state of the art of their glycosidation is also provided.
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Affiliation(s)
- Kler Huonnic
- School
of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| | - Bruno Linclau
- School
of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
- Department
of Organic and Macromolecular Chemistry, Ghent University, Campus Sterre, Krijgslaan 281-S4, Ghent, 9000, Belgium
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16
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Jaeschke SO, Lindhorst TK, Auer A. Between Two Chairs: Combination of Theory and Experiment for the Determination of the Conformational Dynamics of Xylosides. Chemistry 2022; 28:e202201544. [PMID: 35754398 PMCID: PMC9804333 DOI: 10.1002/chem.202201544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Indexed: 01/05/2023]
Abstract
The conformational properties of monosaccharides constitute fundamental features of oligosaccharides. While the energy landscape of monosaccharides can be altered by a specific biochemical environment or by chemical modifications, the analysis of resulting dynamic conformational equilibria is not feasible by experimental means alone. In this work, a series of β-d-xylopyranosides is used to outline how a combination of experimental NMR parameters and computed molecular properties can be used to determine conformers and quantify the composition of conformational equilibria. We demonstrate that identifying the most stable conformers using energy calculations is challenging and computing of NMR shieldings is typically not sensitive enough. On the other hand, computed spin-spin coupling constants for the xyloside ring can be used to unambiguously assign experimental NMR data of dynamic conformational equilibria and quantify the ratio of different conformers in the mixture. As a proof of principle, this procedure allowed to analyze a hitherto unknown dynamic equilibrium of a diamino-xyloside as a precursor of a molecular switch.
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Affiliation(s)
- Sven Ole Jaeschke
- Otto Diels Institute of Organic ChemistryChristiana Albertina University of KielOtto-Hahn-Platz 3–424118KielGermany
| | - Thisbe K. Lindhorst
- Otto Diels Institute of Organic ChemistryChristiana Albertina University of KielOtto-Hahn-Platz 3–424118KielGermany
| | - Alexander Auer
- Max-Planck-Institut für KohlenforschungKaiser-Wilhelm-Platz 145470Mülheim an der RuhrGermany
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17
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Mukherjee S, Jana S, Khawas S, Kicuntod J, Marschall M, Ray B, Ray S. Synthesis, molecular features and biological activities of modified plant polysaccharides. Carbohydr Polym 2022; 289:119299. [DOI: 10.1016/j.carbpol.2022.119299] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 02/23/2022] [Accepted: 02/24/2022] [Indexed: 12/17/2022]
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18
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Meredith R, Carmichael I, Serianni AS. Nonconventional NMR Spin-Coupling Constants in Oligosaccharide Conformational Modeling: Structural Dependencies Determined from Density Functional Theory Calculations. ACS OMEGA 2022; 7:23950-23966. [PMID: 35847250 PMCID: PMC9280969 DOI: 10.1021/acsomega.2c02793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Nonconventional NMR spin-coupling constants were investigated to determine their potential as conformational constraints in MA'AT modeling of the O-glycosidic linkages of oligosaccharides. Four (1 J C1',H1', 1 J C1',C2', 2 J C1',H2', and 2 J C2',H1') and eight (1 J C4,H4, 1 J C3,C4, 1 J C4,C5, 2 J C3,H4, 2 J C4,H3, 2 J C5,H4, 2 J C4,H5, and 2 J C3,C5) spin-couplings in methyl β-d-galactopyranosyl-(1→4)-β-d-glucopyranoside (methyl β-lactoside) were calculated using density functional theory (DFT) to determine their dependencies on O-glycosidic linkage C-O torsion angles, ϕ and ψ, respectively. Long-range 4 J H1',H4 was also examined as a potential conformational constraint of either ϕ or ψ. Secondary effects of exocyclic (hydroxyl) C-O bond rotation within or proximal to these coupling pathways were investigated. Based on the findings of methyl β-lactoside, analogous J-couplings were studied in five additional two-bond O-glycosidic linkages [βGlcNAc-(1→4)-βMan, 2-deoxy-βGlc-(1→4)-βGlc, αMan-(1→3)-βMan, αMan-(1→2)-αMan, and βGlcNAc(1→2)-αMan] to determine whether the coupling behaviors observed in methyl β-lactoside were more broadly observed. Of the 13 nonconventional J-couplings studied, 7 exhibit properties that may be useful in future MA'AT modeling of O-glycosidic linkages, none of which involve coupling pathways that include the linkage C-O bonds. The findings also provide new insights into the general effects of exocyclic C-O bond conformation on the magnitude of experimental spin-couplings in saccharides and other hydroxyl-containing molecules.
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Affiliation(s)
- Reagan
J. Meredith
- Department
of Chemistry and Biochemistry, University
of Notre Dame, Notre
Dame, Indiana 46556-5670, United States
| | - Ian Carmichael
- Radiation
Laboratory, University of Notre Dame, Notre Dame, Indiana 46556-5670, United States
| | - Anthony S. Serianni
- Department
of Chemistry and Biochemistry, University
of Notre Dame, Notre
Dame, Indiana 46556-5670, United States
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19
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Luo Y, Zhao X, Gao Z, Wang H, Liu Y, Guo C, Pan Y. Pd nanoparticles decorated thiol-functionalized MOF as an efficient matrix for differentiation and quantitation of oligosaccharide isomers by laser desorption/ionization mass spectrometry. Anal Chim Acta 2022; 1202:339665. [DOI: 10.1016/j.aca.2022.339665] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/22/2022] [Accepted: 02/26/2022] [Indexed: 11/27/2022]
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20
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Feng X, Li F, Ding M, Zhang R, Shi T, Lu Y, Jiang W. Molecular dynamic simulation: Study on the recognition mechanism of linear β-(1 → 3)-D-glucan by Dectin-1. Carbohydr Polym 2022; 286:119276. [DOI: 10.1016/j.carbpol.2022.119276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 02/13/2022] [Accepted: 02/18/2022] [Indexed: 12/26/2022]
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21
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Poveda A, Fittolani G, Seeberger PH, Delbianco M, Jiménez-Barbero J. The Flexibility of Oligosaccharides Unveiled Through Residual Dipolar Coupling Analysis. Front Mol Biosci 2021; 8:784318. [PMID: 34859057 PMCID: PMC8631391 DOI: 10.3389/fmolb.2021.784318] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 10/14/2021] [Indexed: 11/13/2022] Open
Abstract
The intrinsic flexibility of glycans complicates the study of their structures and dynamics, which are often important for their biological function. NMR has provided insights into the conformational, dynamic and recognition features of glycans, but suffers from severe chemical shift degeneracy. We employed labelled glycans to explore the conformational behaviour of a β(1-6)-Glc hexasaccharide model through residual dipolar couplings (RDCs). RDC delivered information on the relative orientation of specific residues along the glycan chain and provided experimental clues for the existence of certain geometries. The use of two different aligning media demonstrated the adaptability of flexible oligosaccharide structures to different environments.
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Affiliation(s)
- Ana Poveda
- CICbioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - 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
| | - 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
| | - Martina Delbianco
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Potsdam, Germany
| | - Jesús Jiménez-Barbero
- CICbioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, Spain.,Department of Organic Chemistry II, Faculty of Science and Technology, University of the Basque Country, EHU-UPV, Leioa, Spain.,Centro de Investigacion Biomedica En Red de Enfermedades Respiratorias, Madrid, Spain
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22
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Exploiting non-covalent interactions in selective carbohydrate synthesis. Nat Rev Chem 2021; 5:792-815. [PMID: 37117666 DOI: 10.1038/s41570-021-00324-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/10/2021] [Indexed: 02/08/2023]
Abstract
Non-covalent interactions (NCIs) are a vital component of biological bond-forming events, and have found important applications in multiple branches of chemistry. In recent years, the biomimetic exploitation of NCIs in challenging glycosidic bond formation and glycofunctionalizations has attracted significant interest across diverse communities of organic and carbohydrate chemists. This emerging theme is a major new direction in contemporary carbohydrate chemistry, and is rapidly gaining traction as a robust strategy to tackle long-standing issues such as anomeric and site selectivity. This Review thus seeks to provide a bird's-eye view of wide-ranging advances in harnessing NCIs within the broad field of synthetic carbohydrate chemistry. These include the exploitation of NCIs in non-covalent catalysed glycosylations, in non-covalent catalysed glycofunctionalizations, in aglycone delivery, in stabilization of intermediates and transition states, in the existence of intramolecular hydrogen bonding networks and in aggregation by hydrogen bonds. In addition, recent emerging opportunities in exploiting halogen bonding and other unconventional NCIs, such as CH-π, cation-π and cation-n interactions, in various aspects of carbohydrate chemistry are also examined.
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23
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Feng X, Li F, Ding M, Zhang R, Shi T, Jiang W. Molecular dynamic simulation: Structural insights of multi-stranded curdlan in aqueous solution. Carbohydr Polym 2021; 261:117844. [PMID: 33766340 DOI: 10.1016/j.carbpol.2021.117844] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/01/2021] [Accepted: 02/18/2021] [Indexed: 12/28/2022]
Abstract
In this work, by using molecular dynamic simulation we provide microscale structure information which helps to reveal the molecular mechanisms concerning the multi-chain conformational behavior of short curdlan. Through simulations starting with different conformations of curldan dodecasaccharides, it is found that the right-handed triple helix is thermodynamically the most stable conformation in aqueous solutions, which is well maintained and stabilized by an inter-strand hydrogen bonding network of the C2 hydroxyls. Unlike any predicted forms, the inter-strand hydrogen bonds exhibit a left-handed double helix pattern with preferred global orientations. Temperature REMD results suggest that the formation of triple helix is temperature sensitive, but the already formed triple helix is not. Investigation of curdlan with numbers of repeating units from 3 to 12 captures a critical value of 6, which in a way elucidates the relationship between the formation of triple helix and the chain length.
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Affiliation(s)
- Xuan Feng
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, PR China; School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei 230026, PR China
| | - Fan Li
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, PR China
| | - Mingming Ding
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, PR China
| | - Ran Zhang
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, PR China.
| | - Tongfei Shi
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, PR China; School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei 230026, PR China.
| | - Wei Jiang
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, PR China; School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei 230026, PR China
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24
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Zamakhaeva S, Chaton CT, Rush JS, Ajay Castro S, Kenner CW, Yarawsky AE, Herr AB, van Sorge NM, Dorfmueller HC, Frolenkov GI, Korotkov KV, Korotkova N. Modification of cell wall polysaccharide guides cell division in Streptococcus mutans. Nat Chem Biol 2021; 17:878-887. [PMID: 34045745 DOI: 10.1038/s41589-021-00803-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 04/21/2021] [Indexed: 02/07/2023]
Abstract
In ovoid-shaped, Gram-positive bacteria, MapZ guides FtsZ-ring positioning at cell equators. The cell wall of the ovococcus Streptococcus mutans contains peptidoglycan decorated with serotype c carbohydrates (SCCs). In the present study, we identify the major cell separation autolysin AtlA as an SCC-binding protein. AtlA binding to SCC is attenuated by the glycerol phosphate (GroP) modification. Using fluorescently labeled AtlA constructs, we mapped SCC distribution on the streptococcal surface, revealing enrichment of GroP-deficient immature SCCs at the cell poles and equators. The immature SCCs co-localize with MapZ at the equatorial rings throughout the cell cycle. In GroP-deficient mutants, AtlA is mislocalized, resulting in dysregulated cellular autolysis. These mutants display morphological abnormalities associated with MapZ mislocalization, leading to FtsZ-ring misplacement. Altogether, our data support a model in which maturation of a cell wall polysaccharide provides the molecular cues for the recruitment of cell division machinery, ensuring proper daughter cell separation and FtsZ-ring positioning.
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Affiliation(s)
- Svetlana Zamakhaeva
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky, Lexington, KY, USA
| | - Catherine T Chaton
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | - Jeffrey S Rush
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | - Sowmya Ajay Castro
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Cameron W Kenner
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky, Lexington, KY, USA
| | - Alexander E Yarawsky
- Divisions of Immunobiology and Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Andrew B Herr
- Divisions of Immunobiology and Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Nina M van Sorge
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,Netherlands Reference Laboratory for Bacterial Meningitis, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Helge C Dorfmueller
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | | | - Konstantin V Korotkov
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | - Natalia Korotkova
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky, Lexington, KY, USA. .,Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA.
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25
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Manabe Y. Chemical Biology Study on N-glycans. TRENDS GLYCOSCI GLYC 2021. [DOI: 10.4052/tigg.2109.2j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Yoshiyuki Manabe
- Department of Chemistry, Graduate School of Science, Osaka University
- Core for Medicine and Science Collaborative Research and Education, Project Research Center for Fundamental Sciences, Osaka University
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26
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Manabe Y. Chemical Biology Study on N-glycans. TRENDS GLYCOSCI GLYC 2021. [DOI: 10.4052/tigg.2109.2e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Yoshiyuki Manabe
- Department of Chemistry, Graduate School of Science, Osaka University
- Core for Medicine and Science Collaborative Research and Education, Project Research Center for Fundamental Sciences, Osaka University
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Watanabe T, Yagi H, Yanaka S, Yamaguchi T, Kato K. Comprehensive characterization of oligosaccharide conformational ensembles with conformer classification by free-energy landscape via reproductive kernel Hilbert space. Phys Chem Chem Phys 2021; 23:9753-9760. [PMID: 33881019 DOI: 10.1039/d0cp06448c] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Oligosaccharides play versatile roles in various biological systems but are difficult to characterize from a structural viewpoint due to their remarkable degrees of freedom in internal motion. Therefore, molecular dynamics simulations have been widely used to delineate the dynamic conformations of oligosaccharides. However, hardly any methods have thus far been available for the comprehensive characterization of simulation-derived conformational ensembles of oligosaccharides. In this research, we attempted to develop a non-linear multivariate analysis by employing a kernel method using two homologous high-mannose-type oligosaccharides composed of ten and eleven residues as model molecules. These oligosaccharides' conformers derived from simulations were mapped into reproductive kernel Hilbert space with a positive definite function in which all required non-redundant variables for describing the oligosaccharide conformations can be treated in a non-biased manner. By applying Gaussian mixture model clustering, the oligosaccharide conformers were successfully classified by different funnels in the free-energy landscape, enabling a systematic comparison of conformational ensembles of the homologous oligosaccharides. The results shed light on the contributions of intraresidue conformational factors such as the hydroxyl group orientation and/or ring puckering state to their global conformational dynamics. Our methodology will open opportunities to explore oligosaccharides' conformational spaces, and more generally, molecules with high degrees of motional freedom.
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Affiliation(s)
- Tokio Watanabe
- Faculty and Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-Dori, Mizuho-Ku, Nagoya, Aichi 467-8603, Japan.
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28
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Shirakawa A, Manabe Y, Fukase K. Recent Advances in the Chemical Biology of N-Glycans. Molecules 2021; 26:molecules26041040. [PMID: 33669465 PMCID: PMC7920464 DOI: 10.3390/molecules26041040] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/08/2021] [Accepted: 02/14/2021] [Indexed: 12/19/2022] Open
Abstract
Asparagine-linked N-glycans on proteins have diverse structures, and their functions vary according to their structures. In recent years, it has become possible to obtain high quantities of N-glycans via isolation and chemical/enzymatic/chemoenzymatic synthesis. This has allowed for progress in the elucidation of N-glycan functions at the molecular level. Interaction analyses with lectins by glycan arrays or nuclear magnetic resonance (NMR) using various N-glycans have revealed the molecular basis for the recognition of complex structures of N-glycans. Preparation of proteins modified with homogeneous N-glycans revealed the influence of N-glycan modifications on protein functions. Furthermore, N-glycans have potential applications in drug development. This review discusses recent advances in the chemical biology of N-glycans.
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Affiliation(s)
- Asuka Shirakawa
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan;
| | - Yoshiyuki Manabe
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan;
- Core for Medicine and Science Collaborative Research and Education, Project Research Center for Fundamental Sciences, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
- Correspondence: (Y.M.); (K.F.); Tel.: +81-6-6850-5391 (Y.M.); +81-6-6850-5388 (K.F.)
| | - Koichi Fukase
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan;
- Core for Medicine and Science Collaborative Research and Education, Project Research Center for Fundamental Sciences, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
- Correspondence: (Y.M.); (K.F.); Tel.: +81-6-6850-5391 (Y.M.); +81-6-6850-5388 (K.F.)
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29
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Gim S, Fittolani G, Nishiyama Y, Seeberger PH, Ogawa Y, Delbianco M. Supramolecular Assembly and Chirality of Synthetic Carbohydrate Materials. Angew Chem Int Ed Engl 2020; 59:22577-22583. [PMID: 32881205 PMCID: PMC7756587 DOI: 10.1002/anie.202008153] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 08/03/2020] [Indexed: 11/12/2022]
Abstract
Hierarchical carbohydrate architectures serve multiple roles in nature. Hardly any correlations between the carbohydrate chemical structures and the material properties are available due to the lack of standards and suitable analytic techniques. Therefore, designer carbohydrate materials remain highly unexplored, as compared to peptides and nucleic acids. A synthetic D-glucose disaccharide, DD, was chosen as a model to explore carbohydrate materials. Microcrystal electron diffraction (MicroED), optimized for oligosaccharides, revealed that DD assembled into highly crystalline left-handed helical fibers. The supramolecular architecture was correlated to the local crystal organization, allowing for the design of the enantiomeric right-handed fibers, based on the L-glucose disaccharide, LL, or flat lamellae, based on the racemic mixture. Tunable morphologies and mechanical properties suggest the potential of carbohydrate materials for nanotechnology applications.
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Affiliation(s)
- Soeun Gim
- Department of Biomolecular SystemsMax-Planck-Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
- Department of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
| | - Giulio Fittolani
- Department of Biomolecular SystemsMax-Planck-Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
- Department of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
| | | | - Peter H. Seeberger
- Department of Biomolecular SystemsMax-Planck-Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
- Department of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
| | - Yu Ogawa
- Univ. Grenoble AlpesCNRSCERMAV38000GrenobleFrance
| | - Martina Delbianco
- Department of Biomolecular SystemsMax-Planck-Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
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30
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Scherbinina SI, Toukach PV. Three-Dimensional Structures of Carbohydrates and Where to Find Them. Int J Mol Sci 2020; 21:E7702. [PMID: 33081008 PMCID: PMC7593929 DOI: 10.3390/ijms21207702] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 02/06/2023] Open
Abstract
Analysis and systematization of accumulated data on carbohydrate structural diversity is a subject of great interest for structural glycobiology. Despite being a challenging task, development of computational methods for efficient treatment and management of spatial (3D) structural features of carbohydrates breaks new ground in modern glycoscience. This review is dedicated to approaches of chemo- and glyco-informatics towards 3D structural data generation, deposition and processing in regard to carbohydrates and their derivatives. Databases, molecular modeling and experimental data validation services, and structure visualization facilities developed for last five years are reviewed.
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Affiliation(s)
- Sofya I. Scherbinina
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninsky prospect 47, 119991 Moscow, Russia
- Higher Chemical College, D. Mendeleev University of Chemical Technology of Russia, Miusskaya Square 9, 125047 Moscow, Russia
| | - Philip V. Toukach
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninsky prospect 47, 119991 Moscow, Russia
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31
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Gim S, Fittolani G, Nishiyama Y, Seeberger PH, Ogawa Y, Delbianco M. Supramolecular Assembly and Chirality of Synthetic Carbohydrate Materials. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202008153] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Soeun Gim
- Department of Biomolecular Systems Max-Planck-Institute of Colloids and Interfaces Am Mühlenberg 1 14476 Potsdam Germany
- Department of Chemistry and Biochemistry Freie Universität Berlin Arnimallee 22 14195 Berlin Germany
| | - Giulio Fittolani
- Department of Biomolecular Systems Max-Planck-Institute of Colloids and Interfaces Am Mühlenberg 1 14476 Potsdam Germany
- Department of Chemistry and Biochemistry Freie Universität Berlin Arnimallee 22 14195 Berlin Germany
| | | | - Peter H. Seeberger
- Department of Biomolecular Systems Max-Planck-Institute of Colloids and Interfaces Am Mühlenberg 1 14476 Potsdam Germany
- Department of Chemistry and Biochemistry Freie Universität Berlin Arnimallee 22 14195 Berlin Germany
| | - Yu Ogawa
- Univ. Grenoble Alpes CNRS CERMAV 38000 Grenoble France
| | - Martina Delbianco
- Department of Biomolecular Systems Max-Planck-Institute of Colloids and Interfaces Am Mühlenberg 1 14476 Potsdam Germany
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