1
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Edgecomb J, Nguyen DT, Tan S, Murugesan V, Johnson GE, Prabhakaran V. Electrochemical Imaging of Precisely-Defined Redox and Reactive Interfaces. Angew Chem Int Ed Engl 2024; 63:e202405846. [PMID: 38871656 DOI: 10.1002/anie.202405846] [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: 03/26/2024] [Revised: 06/13/2024] [Accepted: 06/13/2024] [Indexed: 06/15/2024]
Abstract
Understanding the diverse electrochemical reactions occurring at electrode-electrolyte interfaces (EEIs) is a critical challenge to developing more efficient energy conversion and storage technologies. Establishing a predictive molecular-level understanding of solid electrolyte interphases (SEIs) is challenging due to the presence of multiple intertwined chemical and electrochemical processes occurring at battery electrodes. Similarly, chemical conversions in reactive electrochemical systems are often influenced by the heterogeneous distribution of active sites, surface defects, and catalyst particle sizes. In this mini review, we highlight an emerging field of interfacial science that isolates the impact of specific chemical species by preparing precisely-defined EEIs and visualizing the reactivity of their individual components using single-entity characterization techniques. We highlight the broad applicability and versatility of these methods, along with current state-of-the-art instrumentation and future opportunities for these approaches to address key scientific challenges related to batteries, chemical separations, and fuel cells. We establish that controlled preparation of well-defined electrodes combined with single entity characterization will be crucial to filling key knowledge gaps and advancing the theories used to describe and predict chemical and physical processes occurring at EEIs and accelerating new materials discovery for energy applications.
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Affiliation(s)
- Joseph Edgecomb
- Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | | | - Shuai Tan
- Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | | | - Grant E Johnson
- Pacific Northwest National Laboratory, Richland, WA 99352, USA
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2
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Esat T, Borodin D, Oh J, Heinrich AJ, Tautz FS, Bae Y, Temirov R. A quantum sensor for atomic-scale electric and magnetic fields. NATURE NANOTECHNOLOGY 2024:10.1038/s41565-024-01724-z. [PMID: 39054385 DOI: 10.1038/s41565-024-01724-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 06/18/2024] [Indexed: 07/27/2024]
Abstract
The detection of faint magnetic fields from single-electron and nuclear spins at the atomic scale is a long-standing challenge in physics. While current mobile quantum sensors achieve single-electron spin sensitivity, atomic spatial resolution remains elusive for existing techniques. Here we fabricate a single-molecule quantum sensor at the apex of the metallic tip of a scanning tunnelling microscope by attaching Fe atoms and a PTCDA (3,4,9,10-perylenetetracarboxylic-dianhydride) molecule to the tip apex. We address the molecular spin by electron spin resonance and achieve ~100 neV resolution in energy. In a proof-of-principle experiment, we measure the magnetic and electric dipole fields emanating from a single Fe atom and an Ag dimer on an Ag(111) surface with sub-angstrom spatial resolution. Our method enables atomic-scale quantum sensing experiments of electric and magnetic fields on conducting surfaces and may find applications in the sensing of spin-labelled biomolecules and of spin textures in quantum materials.
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Affiliation(s)
- Taner Esat
- Peter Grünberg Institute (PGI-3), Forschungszentrum Jülich, Jülich, Germany.
- Jülich Aachen Research Alliance (JARA), Fundamentals of Future Information Technology, Jülich, Germany.
| | - Dmitriy Borodin
- Center for Quantum Nanoscience (QNS), Institute for Basic Science (IBS), Seoul, South Korea
- Department of Physics, Ewha Womans University, Seoul, South Korea
| | - Jeongmin Oh
- Center for Quantum Nanoscience (QNS), Institute for Basic Science (IBS), Seoul, South Korea
- Department of Physics, Ewha Womans University, Seoul, South Korea
| | - Andreas J Heinrich
- Center for Quantum Nanoscience (QNS), Institute for Basic Science (IBS), Seoul, South Korea.
- Department of Physics, Ewha Womans University, Seoul, South Korea.
| | - F Stefan Tautz
- Peter Grünberg Institute (PGI-3), Forschungszentrum Jülich, Jülich, Germany
- Jülich Aachen Research Alliance (JARA), Fundamentals of Future Information Technology, Jülich, Germany
- Experimentalphysik IV A, RWTH Aachen University, Aachen, Germany
| | - Yujeong Bae
- Center for Quantum Nanoscience (QNS), Institute for Basic Science (IBS), Seoul, South Korea.
- Department of Physics, Ewha Womans University, Seoul, South Korea.
- Empa, Swiss Federal Laboratories for Materials Science and Technology, nanotech@surfaces Laboratory, Dübendorf, Switzerland.
| | - Ruslan Temirov
- Peter Grünberg Institute (PGI-3), Forschungszentrum Jülich, Jülich, Germany
- Jülich Aachen Research Alliance (JARA), Fundamentals of Future Information Technology, Jülich, Germany
- Faculty of Mathematics and Natural Sciences, Institute of Physics II, University of Cologne, Cologne, Germany
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3
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Mallada B, Villalobos F, Donoso B, Casares R, Longhi G, Mendieta-Moreno JI, Jiménez-Martín A, Haïdour A, Seepersaud R, Rajagopal L, de la Torre B, Millán A, Cuerva JM. Single-Molecule Identification of the Isomers of a Lipidic Antibody Activator. J Phys Chem Lett 2024; 15:6935-6942. [PMID: 38935930 PMCID: PMC11247479 DOI: 10.1021/acs.jpclett.4c00164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 03/29/2024] [Accepted: 05/03/2024] [Indexed: 06/29/2024]
Abstract
Molecular structural elucidation can be accomplished by different techniques, such as nuclear magnetic resonance or X-ray diffraction. However, the former does not give information about the three-dimensional atomic arrangement, and the latter needs crystallizable solid samples. An alternative is direct, real-space visualization of the molecules by cryogenic scanning tunneling microscopy (STM). This technique is usually limited to thermally robust molecules because an annealing step is required for sample deposition. A landmark development has been the coupling of STM with electrospray deposition (ESD), which smooths the process and widens the scope of the visualization technique. In this work, we present the on-surface characterization of air-, light-, and temperature-sensitive rhamnopolyene with relevance in molecular biology. Supported by theoretical calculations, we characterize two isomers of this flexible molecule, confirming the potential of the technique to inspect labile, non-crystallizable compounds.
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Affiliation(s)
- Benjamin Mallada
- Institute
of Physics, Czech Academy of Sciences, 16200 Prague, Czech Republic
- Regional
Centre of Advanced Technologies and Materials, Czech Advanced Technology
and Research Institute (CATRIN), Palacký
University Olomouc, 78371 Olomouc, Czech Republic
| | - Federico Villalobos
- Departamento
de Química Orgánica, Unidad de Excelencia de Química
Aplicada a la Biomedicina y Medioambiente, C. U. Fuentenueva, Universidad de Granada, 18071 Granada, Spain
| | - Beatriz Donoso
- Departamento
de Química Orgánica, Unidad de Excelencia de Química
Aplicada a la Biomedicina y Medioambiente, C. U. Fuentenueva, Universidad de Granada, 18071 Granada, Spain
| | - Raquel Casares
- Departamento
de Química Orgánica, Unidad de Excelencia de Química
Aplicada a la Biomedicina y Medioambiente, C. U. Fuentenueva, Universidad de Granada, 18071 Granada, Spain
| | - Giovanna Longhi
- Dipartimento
di Medicina Molecolare e Traslazionale, Universitá di Brescia, Viale Europa 11, 25121 Brescia, Italy
| | - Jesús I. Mendieta-Moreno
- Instituto
de Ciencia de Materiales de Madrid (ICMM), Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain
| | - Alejandro Jiménez-Martín
- Institute
of Physics, Czech Academy of Sciences, 16200 Prague, Czech Republic
- Regional
Centre of Advanced Technologies and Materials, Czech Advanced Technology
and Research Institute (CATRIN), Palacký
University Olomouc, 78371 Olomouc, Czech Republic
- Faculty
of Nuclear Sciences and Physical Engineering, Czech Technical University, 11519 Prague, Czech
Republic
| | - Ali Haïdour
- Unidad
de Resonancia Magnética Nuclear, Centro de Instrumentación
Científica, Universidad de Granada, Paseo Juan Osorio s/n, 18071 Granada, Spain
| | - Ravin Seepersaud
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
| | - Lakshmi Rajagopal
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
- Department
of Global Health, University of Washington, Seattle, Washington 98105, United States
- Department
of Pediatrics, University of Washington, Seattle, Washington 98105, United States
| | - Bruno de la Torre
- Regional
Centre of Advanced Technologies and Materials, Czech Advanced Technology
and Research Institute (CATRIN), Palacký
University Olomouc, 78371 Olomouc, Czech Republic
| | - Alba Millán
- Departamento
de Química Orgánica, Unidad de Excelencia de Química
Aplicada a la Biomedicina y Medioambiente, C. U. Fuentenueva, Universidad de Granada, 18071 Granada, Spain
| | - Juan M. Cuerva
- Departamento
de Química Orgánica, Unidad de Excelencia de Química
Aplicada a la Biomedicina y Medioambiente, C. U. Fuentenueva, Universidad de Granada, 18071 Granada, Spain
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4
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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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5
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Kizer ME, R. Dwyer J. Editors' Choice-Perspective-Deciphering the Glycan Kryptos by Solid-State Nanopore Single-Molecule Sensing: A Call for Integrated Advancements Across Glyco- and Nanopore Science. ECS SENSORS PLUS 2024; 3:020604. [PMID: 38799647 PMCID: PMC11125560 DOI: 10.1149/2754-2726/ad49b0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 05/07/2024] [Indexed: 05/29/2024]
Abstract
Glycans, or complex carbohydrates, are information-rich biopolymers critical to many biological processes and with considerable importance in pharmaceutical therapeutics. Our understanding, though, is limited compared to other biomolecules such as DNA and proteins. The greater complexity of glycan structure and the limitations of conventional chemical analysis methods hinder glycan studies. Auspiciously, nanopore single-molecule sensors-commercially available for DNA sequencing-hold great promise as a tool for enabling and advancing glycan analysis. We focus on two key areas to advance nanopore glycan characterization: molecular surface coatings to enhance nanopore performance including by molecular recognition, and high-quality glycan chemical standards for training.
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Affiliation(s)
- Megan E. Kizer
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States of America
| | - Jason R. Dwyer
- Department of Chemistry, University of Rhode Island, Kingston, Rhode Island, 02881, United States of America
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6
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Yang G, Liu Y, Hu Y, Yuan Y, Qin Y, Li Q, Ma S. Bio-soft matter derived from traditional Chinese medicine: Characterizations of hierarchical structure, assembly mechanism, and beyond. J Pharm Anal 2024; 14:100943. [PMID: 39005842 PMCID: PMC11246065 DOI: 10.1016/j.jpha.2024.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 01/03/2024] [Accepted: 01/31/2024] [Indexed: 07/16/2024] Open
Abstract
Structural and functional explorations on bio-soft matter such as micelles, vesicles, nanoparticles, aggregates or polymers derived from traditional Chinese medicine (TCM) has emerged as a new topic in the field of TCM. The discovery of such cross-scaled bio-soft matter may provide a unique perspective for unraveling the new effective material basis of TCM as well as developing innovative medicine and biomaterials. Despite the rapid rise of TCM-derived bio-soft matter, their hierarchical structure and assembly mechanism must be unambiguously probed for a further in-depth understanding of their pharmacological activity. In this review, the current emerged TCM-derived bio-soft matter assembled from either small molecules or macromolecules is introduced, and particularly the unambiguous elucidation of their hierarchical structure and assembly mechanism with combined electron microscopic and spectroscopic techniques is depicted. The pros and cons of each technique are also discussed. The future challenges and perspective of TCM-derived bio-soft matter are outlined, particularly the requirement for their precise in situ structural determination is highlighted.
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Affiliation(s)
- Guiya Yang
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Yue Liu
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Yuying Hu
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Yue Yuan
- Tianjin Key Laboratory of Therapeutic Substance of Traditional Chinese Medicine, School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Yunan Qin
- Collaborative Innovation Center for Advanced Organic Chemical Materials Co-constructed by the Province and Ministry, Ministry-of-Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, College of Chemistry and Chemical Engineering, Hubei University, Wuhan, 430062, China
| | - Quan Li
- Tianjin Key Laboratory of Therapeutic Substance of Traditional Chinese Medicine, School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Shuangcheng Ma
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 102488, China
- Institute for Control of Chinese Traditional Medicine and Ethnic Medicine, National Institutes for Food and Drug Control, Beijing, 100050, China
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7
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Boerjan W, Burlat V, Cosgrove DJ, Dunand C, Dupree P, Haas KT, Ingram G, Jamet E, Mohnen D, Moussu S, Peaucelle A, Persson S, Voiniciuc C, Höfte H. Top five unanswered questions in plant cell surface research. Cell Surf 2024; 11:100121. [PMID: 38405175 PMCID: PMC10885547 DOI: 10.1016/j.tcsw.2024.100121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/12/2024] [Accepted: 02/12/2024] [Indexed: 02/27/2024] Open
Abstract
Plant cell wall researchers were asked their view on what the major unanswered questions are in their field. This article summarises the feedback that was received from them in five questions. In this issue you can find equivalent syntheses for researchers working on bacterial, unicellular parasite and fungal systems.
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Affiliation(s)
- Wout Boerjan
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Gent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Gent, Belgium
| | - Vincent Burlat
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, Auzeville-Tolosane, France
| | - Daniel J. Cosgrove
- Department of Biology, Pennsylvania State University, University Park, PA 16870, the United States of America
| | - Christophe Dunand
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, Auzeville-Tolosane, France
| | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Kalina T. Haas
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Gwyneth Ingram
- Laboratoire Reproduction et Développement des Plantes, ENS de Lyon, CNRS, INRAE, UCBL, Lyon, France
| | - Elisabeth Jamet
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, Auzeville-Tolosane, France
| | - Debra Mohnen
- Complex Carbohydrate Research Center and Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Steven Moussu
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, Auzeville-Tolosane, France
| | - Alexis Peaucelle
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Staffan Persson
- Copenhagen Plant Science Center (CPSC), Department of Plant & Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Cătălin Voiniciuc
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, the United States of America
| | - Herman Höfte
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
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8
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Elzinga J, Narimatsu Y, de Haan N, Clausen H, de Vos WM, Tytgat HLP. Binding of Akkermansia muciniphila to mucin is O-glycan specific. Nat Commun 2024; 15:4582. [PMID: 38811534 PMCID: PMC11137150 DOI: 10.1038/s41467-024-48770-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 05/09/2024] [Indexed: 05/31/2024] Open
Abstract
The intestinal anaerobic bacterium Akkermansia muciniphila is specialized in the degradation of mucins, which are heavily O-glycosylated proteins that constitute the major components of the mucus lining the intestine. Despite that adhesion to mucins is considered critical for the persistence of A. muciniphila in the human intestinal tract, our knowledge of how this intestinal symbiont recognizes and binds to mucins is still limited. Here, we first show that the mucin-binding properties of A. muciniphila are independent of environmental oxygen concentrations and not abolished by pasteurization. We then dissected the mucin-binding properties of pasteurized A. muciniphila by use of a recently developed cell-based mucin array that enables display of the tandem repeats of human mucins with distinct O-glycan patterns and structures. We found that A. muciniphila recognizes the unsialylated LacNAc (Galβ1-4GlcNAcβ1-R) disaccharide selectively on core2 and core3 O-glycans. This disaccharide epitope is abundantly found on human colonic mucins capped by sialic acids, and we demonstrated that endogenous A. muciniphila neuraminidase activity can uncover the epitope and promote binding. In summary, our study provides insights into the mucin-binding properties important for colonization of a key mucin-foraging bacterium.
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Affiliation(s)
- Janneke Elzinga
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands.
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Yoshiki Narimatsu
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- GlycoDisplay ApS, Copenhagen, Denmark
| | - Noortje de Haan
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Hanne L P Tytgat
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands.
- Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland.
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9
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Geue N. Modern Electrospray Ionization Mass Spectrometry Techniques for the Characterization of Supramolecules and Coordination Compounds. Anal Chem 2024; 96:7332-7341. [PMID: 38686955 PMCID: PMC11099892 DOI: 10.1021/acs.analchem.4c01028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 04/15/2024] [Accepted: 04/17/2024] [Indexed: 05/02/2024]
Abstract
Mass spectrometry is routinely used for myriad applications in clinical, industrial, and research laboratories worldwide. Developments in the areas of ionization sources, high-resolution mass analyzers, tandem mass spectrometry, and ion mobility have significantly extended the repertoire of mass spectrometrists; however, for coordination compounds and supramolecules, mass spectrometry remains underexplored and arguably underappreciated. Here, the reader is guided through different tools of modern electrospray ionization mass spectrometry that are suitable for larger inorganic complexes. All steps, from sample preparation and technical details to data analysis and interpretation are discussed. The main target audience of this tutorial is synthetic chemists as well as technicians/mass spectrometrists with little experience in characterizing labile inorganic compounds.
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Affiliation(s)
- Niklas Geue
- Michael Barber Centre for Collaborative
Mass Spectrometry, Manchester Institute of Biotechnology, Department
of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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10
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Yao G, Ke W, Xia B, Gao Z. Nanopore-based glycan sequencing: state of the art and future prospects. Chem Sci 2024; 15:6229-6243. [PMID: 38699252 PMCID: PMC11062086 DOI: 10.1039/d4sc01466a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 04/02/2024] [Indexed: 05/05/2024] Open
Abstract
Sequencing of biomacromolecules is a crucial cornerstone in life sciences. Glycans, one of the fundamental biomolecules, derive their physiological and pathological functions from their structures. Glycan sequencing faces challenges due to its structural complexity and current detection technology limitations. As a highly sensitive sensor, nanopores can directly convert nucleic acid sequence information into electrical signals, spearheading the revolution of third-generation nucleic acid sequencing technologies. However, their potential for deciphering complex glycans remains untapped. Initial attempts demonstrated the significant sensitivity of nanopores in glycan sensing, which provided the theoretical basis and insights for the realization of nanopore-based glycan sequencing. Here, we present three potential technical routes to employ nanopore technology in glycan sequencing for the first time. The three novel technical routes include: strand sequencing, capturing glycan chains as they translocate through nanopores; sequential hydrolysis sequencing, capturing released monosaccharides one by one; splicing sequencing, mapping signals from hydrolyzed glycan fragments to an oligosaccharide database/library. Designing suitable nanopores, enzymes, and motors, and extracting characteristic signals pose major challenges, potentially aided by artificial intelligence. It would be highly desirable to design an all-in-one high-throughput glycan sequencer instrument by integrating a sample processing unit, nanopore array, and signal acquisition system into a microfluidic device. The nanopore sequencer invention calls for intensive multidisciplinary cooperation including electrochemistry, glycochemistry, engineering, materials, enzymology, etc. Advancing glycan sequencing will promote the development of basic research and facilitate the discovery of glycan-based drugs and disease markers, fostering progress in glycoscience and even life sciences.
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Affiliation(s)
- Guangda Yao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 201203 Shanghai China
- School of Life Science and Technology, Shanghai Tech University 201210 Shanghai China
- Lingang Laboratory 200031 Shanghai China
| | - Wenjun Ke
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 201203 Shanghai China
- University of Chinese Academy of Sciences 100049 Beijing China
| | - Bingqing Xia
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 201203 Shanghai China
- University of Chinese Academy of Sciences 100049 Beijing China
| | - Zhaobing Gao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 201203 Shanghai China
- University of Chinese Academy of Sciences 100049 Beijing China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 528400 Zhongshan China
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11
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Domma AJ, Henderson LA, Nurdin JA, Kamil JP. Uncloaking the viral glycocalyx: How do viruses exploit glycoimmune checkpoints? Adv Virus Res 2024; 119:63-110. [PMID: 38897709 PMCID: PMC11192240 DOI: 10.1016/bs.aivir.2024.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
The surfaces of cells and enveloped viruses alike are coated in carbohydrates that play multifarious roles in infection and immunity. Organisms across all kingdoms of life make use of a diverse set of monosaccharide subunits, glycosidic linkages, and branching patterns to encode information within glycans. Accordingly, sugar-patterning enzymes and glycan binding proteins play integral roles in cell and organismal biology, ranging from glycoprotein quality control within the endoplasmic reticulum to lymphocyte migration, coagulation, inflammation, and tissue homeostasis. Unsurprisingly, genes involved in generating and recognizing oligosaccharide patterns are playgrounds for evolutionary conflicts that abound in cross-species interactions, exemplified by the myriad plant lectins that function as toxins. In vertebrates, glycans bearing acidic nine-carbon sugars called sialic acids are key regulators of immune responses. Various bacterial and fungal pathogens adorn their cells in sialic acids that either mimic their hosts' or are stolen from them. Yet, how viruses commandeer host sugar-patterning enzymes to thwart immune responses remains poorly studied. Here, we review examples of viruses that interact with sialic acid-binding immunoglobulin-like lectins (Siglecs), a family of immune cell receptors that regulate toll-like receptor signaling and govern glycoimmune checkpoints, while highlighting knowledge gaps that merit investigation. Efforts to illuminate how viruses leverage glycan-dependent checkpoints may translate into new clinical treatments that uncloak viral antigens and infected cell surfaces by removing or masking immunosuppressive sialoglycans, or by inhibiting viral gene products that induce their biosynthesis. Such approaches may hold the potential to unleash the immune system to clear long intractable chronic viral infections.
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Affiliation(s)
- Anthony J Domma
- LSU Health Sciences Center at Shreveport, Shreveport, LA, United States
| | | | - Jeffery A Nurdin
- LSU Health Sciences Center at Shreveport, Shreveport, LA, United States
| | - Jeremy P Kamil
- LSU Health Sciences Center at Shreveport, Shreveport, LA, United States.
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12
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Pinkeova A, Kosutova N, Jane E, Lorencova L, Bertokova A, Bertok T, Tkac J. Medical Relevance, State-of-the-Art and Perspectives of "Sweet Metacode" in Liquid Biopsy Approaches. Diagnostics (Basel) 2024; 14:713. [PMID: 38611626 PMCID: PMC11011756 DOI: 10.3390/diagnostics14070713] [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: 02/07/2024] [Revised: 03/23/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
This review briefly introduces readers to an area where glycomics meets modern oncodiagnostics with a focus on the analysis of sialic acid (Neu5Ac)-terminated structures. We present the biochemical perspective of aberrant sialylation during tumourigenesis and its significance, as well as an analytical perspective on the detection of these structures using different approaches for diagnostic and therapeutic purposes. We also provide a comparison to other established liquid biopsy approaches, and we mathematically define an early-stage cancer based on the overall prognosis and effect of these approaches on the patient's quality of life. Finally, some barriers including regulations and quality of clinical validations data are discussed, and a perspective and major challenges in this area are summarised.
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Affiliation(s)
- Andrea Pinkeova
- Institute of Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, 845 38 Bratislava, Slovakia; (A.P.); (N.K.); (E.J.); (L.L.)
- Glycanostics, Ltd., Kudlakova 7, 841 08 Bratislava, Slovakia;
| | - Natalia Kosutova
- Institute of Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, 845 38 Bratislava, Slovakia; (A.P.); (N.K.); (E.J.); (L.L.)
| | - Eduard Jane
- Institute of Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, 845 38 Bratislava, Slovakia; (A.P.); (N.K.); (E.J.); (L.L.)
| | - Lenka Lorencova
- Institute of Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, 845 38 Bratislava, Slovakia; (A.P.); (N.K.); (E.J.); (L.L.)
| | - Aniko Bertokova
- Glycanostics, Ltd., Kudlakova 7, 841 08 Bratislava, Slovakia;
| | - Tomas Bertok
- Institute of Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, 845 38 Bratislava, Slovakia; (A.P.); (N.K.); (E.J.); (L.L.)
| | - Jan Tkac
- Institute of Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, 845 38 Bratislava, Slovakia; (A.P.); (N.K.); (E.J.); (L.L.)
- Glycanostics, Ltd., Kudlakova 7, 841 08 Bratislava, Slovakia;
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Gericke M, Amaral AJR, Budtova T, De Wever P, Groth T, Heinze T, Höfte H, Huber A, Ikkala O, Kapuśniak J, Kargl R, Mano JF, Másson M, Matricardi P, Medronho B, Norgren M, Nypelö T, Nyström L, Roig A, Sauer M, Schols HA, van der Linden J, Wrodnigg TM, Xu C, Yakubov GE, Stana Kleinschek K, Fardim P. The European Polysaccharide Network of Excellence (EPNOE) research roadmap 2040: Advanced strategies for exploiting the vast potential of polysaccharides as renewable bioresources. Carbohydr Polym 2024; 326:121633. [PMID: 38142079 DOI: 10.1016/j.carbpol.2023.121633] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/17/2023] [Accepted: 11/21/2023] [Indexed: 12/25/2023]
Abstract
Polysaccharides are among the most abundant bioresources on earth and consequently need to play a pivotal role when addressing existential scientific challenges like climate change and the shift from fossil-based to sustainable biobased materials. The Research Roadmap 2040 of the European Polysaccharide Network of Excellence (EPNOE) provides an expert's view on how future research and development strategies need to evolve to fully exploit the vast potential of polysaccharides as renewable bioresources. It is addressed to academic researchers, companies, as well as policymakers and covers five strategic areas that are of great importance in the context of polysaccharide related research: (I) Materials & Engineering, (II) Food & Nutrition, (III) Biomedical Applications, (IV) Chemistry, Biology & Physics, and (V) Skills & Education. Each section summarizes the state of research, identifies challenges that are currently faced, project achievements and developments that are expected in the upcoming 20 years, and finally provides outlines on how future research activities need to evolve.
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Affiliation(s)
- Martin Gericke
- Friedrich Schiller University of Jena, Institute of Organic Chemistry and Macromolecular Chemistry, Centre of Excellence for Polysaccharide Research, Humboldtstraße 10, D-07743 Jena, Germany
| | - Adérito J R Amaral
- Department of Chemistry, CICECO-Aveiro Institute of Materials, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Tatiana Budtova
- MINES Paris, PSL University, CEMEF - Center for Materials Forming, UMR CNRS 7635, CS 10207, rue Claude Daunesse, 06904 Sophia Antipolis, France
| | - Pieter De Wever
- KU Leuven, Department of Chemical Engineering, Chemical and Biochemical Reactor Engineering and Safety (CREaS), Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Thomas Groth
- Department Biomedical Materials, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, 06099 Halle (Saale), Germany
| | - Thomas Heinze
- Friedrich Schiller University of Jena, Institute of Organic Chemistry and Macromolecular Chemistry, Centre of Excellence for Polysaccharide Research, Humboldtstraße 10, D-07743 Jena, Germany
| | - Herman Höfte
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Anton Huber
- University Graz, Inst.f. Chem./PS&HC - Polysaccharides & Hydrocolloids, Heinrichstrasse 28, 8010 Graz, Austria
| | - Olli Ikkala
- Department of Applied Physics, Aalto University School of Science, FI-00076 Espoo, Finland
| | - Janusz Kapuśniak
- Jan Dlugosz University in Czestochowa, Faculty of Science and Technology, Department of Dietetics and Food Studies, Waszyngtona 4/8, 42-200 Czestochowa, Poland
| | - Rupert Kargl
- Graz University of Technology, Institute of Chemistry and Technology of Biobased Systems, Stremayrgasse 9, A-8010 Graz, Austria
| | - João F Mano
- Department of Chemistry, CICECO-Aveiro Institute of Materials, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Már Másson
- Faculty of Pharmaceutical Sciences, School of Health Sciences, University of Iceland, Hofsvallagata 53, IS-107 Reykjavík, Iceland
| | - Pietro Matricardi
- Sapienza University of Rome, Department of Drug Chemistry and Technologies, P.le A. Moro 5, 00185 Rome, Italy
| | - Bruno Medronho
- MED-Mediterranean Institute for Agriculture, Environment and Development, CHANGE-Global Change and Sustainability Institute, Faculdade de Ciências e Tecnologia, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal; Surface and Colloid Engineering, FSCN Research Center, Mid Sweden University, SE-851 70 Sundsvall, Sweden
| | - Magnus Norgren
- Surface and Colloid Engineering, FSCN Research Center, Mid Sweden University, SE-851 70 Sundsvall, Sweden
| | - Tiina Nypelö
- Chalmers University of Technology, Department of Chemistry and Chemical Engineering, 41296 Gothenburg, Sweden; Aalto University, Department of Bioproducts and Biosystems, 00076 Aalto, Finland
| | - Laura Nyström
- ETH Zurich, Department of Health Sciences and Technology, Schmelzbergstrasse 9, 8092 Zurich, Switzerland
| | - Anna Roig
- Institute of Materials Science of Barcelona (ICMAB-CSIC), 08193 Bellaterra, Spain
| | - Michael Sauer
- University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, Muthgasse 18, 1190 Vienna, Austria
| | - Henk A Schols
- Laboratory of Food Chemistry, Wageningen University and Research, Bornse Weilanden 9, 6708WG Wageningen, the Netherlands
| | | | - Tanja M Wrodnigg
- Graz University of Technology, Institute of Chemistry and Technology of Biobased Systems, Stremayrgasse 9, A-8010 Graz, Austria
| | - Chunlin Xu
- Åbo Akademi University, Laboratory of Natural Materials Technology, Henrikinkatu 2, Turku/Åbo, Finland
| | - Gleb E Yakubov
- Soft Matter Biomaterials and Biointerfaces, Food Structure and Biomaterials Group, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom
| | - Karin Stana Kleinschek
- Graz University of Technology, Institute of Chemistry and Technology of Biobased Systems, Stremayrgasse 9, A-8010 Graz, Austria.
| | - Pedro Fardim
- KU Leuven, Department of Chemical Engineering, Chemical and Biochemical Reactor Engineering and Safety (CREaS), Celestijnenlaan 200F, 3001 Leuven, Belgium
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14
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Ferro F, Spelat R, Pandit A, Martin-Ventura JL, Rabinovich GA, Contessotto P. Glycosylation of blood cells during the onset and progression of atherosclerosis and myocardial infarction. Trends Mol Med 2024; 30:178-196. [PMID: 38142190 DOI: 10.1016/j.molmed.2023.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/27/2023] [Accepted: 11/24/2023] [Indexed: 12/25/2023]
Abstract
Protein glycosylation controls cell-cell and cell-extracellular matrix (ECM) communication in immune, vascular, and inflammatory processes, underlining the critical role of this process in the identification of disease biomarkers and the design of novel therapies. Emerging evidence highlights the critical role of blood cell glycosylation in the pathophysiology of atherosclerosis (ATH) and myocardial infarction (MI). Here, we review the role of glycosylation in the interplay between blood cells, particularly erythrocytes, and endothelial cells (ECs), highlighting the involvement of this critical post/cotranslational modification in settings of cardiovascular disease (CVD). Importantly, we focus on emerging preclinical studies and clinical trials based on glycan-targeted drugs to validate their therapeutic potential. These findings may help establish new trends in preventive medicine and delineate novel targeted therapies in CVD.
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Affiliation(s)
- Federico Ferro
- CÚRAM, SFI Research Centre for Medical Devices, University of Galway, Galway, Ireland; Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Renza Spelat
- CÚRAM, SFI Research Centre for Medical Devices, University of Galway, Galway, Ireland; Neurobiology Sector, International School for Advanced Studies (SISSA), Trieste, Italy
| | - Abhay Pandit
- CÚRAM, SFI Research Centre for Medical Devices, University of Galway, Galway, Ireland
| | - José L Martin-Ventura
- Vascular Research Laboratory, IIS-Fundación Jiménez-Díaz, Madrid, Spain; CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain.
| | - Gabriel A Rabinovich
- Laboratorio de Glicomedicina, Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina; Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.
| | - Paolo Contessotto
- CÚRAM, SFI Research Centre for Medical Devices, University of Galway, Galway, Ireland; Department of Molecular Medicine, University of Padua, Padua, Italy.
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15
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Delbianco M, Ogawa Y. Visualizing the structural diversity of glycoconjugates. Nat Chem Biol 2024; 20:11-12. [PMID: 38092986 DOI: 10.1038/s41589-023-01502-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Affiliation(s)
- Martina Delbianco
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany.
| | - Yu Ogawa
- Univ. Grenoble Alpes, CNRS, CERMAV, Grenoble, France.
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