Article
Chemistry, Applied
Minna Juvonen, Edwin Bakx, Henk Schols, Maija Tenkanen
Summary: This study investigated the potential of using TWIMS and CID-TWIMS-MS/MS to separate cereal-derived isomeric arabinoxylanoligosaccharides (A)XOS. The triand pentasaccharide isomers were distinguishable by the ATDs of the precursor ions, while CID-TWIMS-MS/MS could effectively separate isomeric fragment ions produced from tetra- and pentasaccharide (A)XOS. The base peak mobility spectrum was also introduced as a practical tool for (A)XOS fingerprinting.
Article
Chemistry, Analytical
Erik Saparbaev, Andrei Zviagin, Oleg Boyarkin
Summary: We propose a universal approach for the quantitative identification of different isomeric biomolecules using infrared fragment cold ion spectroscopy. The method utilizes solvent molecules as natural tags, eliminating the need for any special compounds and allowing for the measurement of relative concentrations of isomers.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Analytical
Chuncui Huang, Meijie Hou, Jingyu Yan, Hui Wang, Yu Wang, Cuiyan Cao, Yaojun Wang, Huanyu Gao, Xinyue Ma, Yi Zheng, Dongbo Bu, Wengang Chai, Yan Li, Shiwei Sun
Summary: Accurate identification of glycan structures is challenging due to the existence of multiple isomeric structures in glycan samples. Researchers developed an intelligent group-opting strategy, named GIPS-mix, to assign isomeric glycans within mixtures based on simulated spectra and experimental spectra similarity. If a single group cannot be elected, a tie break is performed by additional MSn scanning using intelligently selected precursors. Through the application of GIPS-mix on standard mixtures and human milk oligosaccharide fractions, high accuracy and efficiency in assigning individual glycans in mixtures were demonstrated.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Jieqiang Zhong, Yifan Huang, Yehia Mechref
Summary: This study presents an efficient derivatization method for discriminating sialic acid linkage isomers on glycopeptides, resulting in increased signal and successful characterization of sialylated glycopeptides from various proteins. The method targets site- and sialic acid linkage-specific profiling of glycosylation, making it a facile and highly reproducible technique.
ANALYTICAL CHEMISTRY
(2021)
Review
Chemistry, Analytical
Yuelin Song, Qingqing Song, Wenjing Liu, Jun Li, Pengfei Tu
Summary: Currently, MS/MS is widely used in metabolomics for the identification of metabolites. However, the structural identification of isomers remains challenging due to the similarity of their MS/MS spectra. Differentiation and identification of isomers using MS/MS can be facilitated by various techniques, including chemical derivatization, ion mobility spectrometry, ion dissociation techniques, and energy-resolved MS. This tutorial provides a comprehensive summary of these cutting-edge techniques and emphasizes the importance of isomeric identification in metabolomics for analytical chemists. (c) 2023 Elsevier B.V. All rights reserved.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Amandine Hueber, Martin Green, Jakub Ujma, Keith Richardson, Yves Gimbert, Nicolas Cenac, Justine Bertrand-Michel, Jean-Claude Tabet
Summary: This study investigates the structural characterization of lipopeptides synthesized from bacteria using mass spectrometry. A particular lipopeptide showed surprising fragmentation pathways, which were analyzed using energy-resolved mass spectrometry. The results provided insights into the mechanisms and structures of the fragmented product ions.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Multidisciplinary Sciences
Lu Li, Cuiji Sun, Yaoting Sun, Zhen Dong, Runxin Wu, Xiaoting Sun, Hanbin Zhang, Wenhao Jiang, Yan Zhou, Xufeng Cen, Shang Cai, Hongguang Xia, Yi Zhu, Tiannan Guo, Kiryl D. Piatkevich
Summary: This paper describes a spatially resolved proteomics method called Expansion Proteomics (ProteomEx), which combines tissue expansion with mass spectrometry-based proteomics. The method allows quantitative profiling of proteome variability in mammalian tissues using manual microsampling, without the need for custom equipment. The authors validated the method by analyzing brain, liver, and breast cancer samples, and demonstrated its utility by identifying proteins associated with Alzheimer's disease in a mouse model.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Analytical
Erik Saparbaev, Ruslan Yamaletdinov, Oleg Boyarkin
Summary: The diverse structures and isomeric nature of lipids provide a wide range of functions in nature, but also present challenges in identification. By using cold ion UV fragmentation spectroscopy of noncovalent complexes with aromatic amino acids and dipeptides, isomeric lipids can be distinguished and quantified. Preselected aromatic sensors sensitive to specific isomers have been used to accurately determine relative concentrations of isomeric glycerophospholipids mixed in solution.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Analytical
Praneeth M. Mendis, Zachary J. Sasiene, David Ropartz, Helene Rogniaux, Glen P. Jackson
Summary: This study successfully coupled charge transfer dissociation-mass spectrometry (CTD-MS) with ultrahigh-performance liquid chromatography (UHPLC) to differentiate isomers of oligogalacturonans derived from citrus pectins. Compared to UHPLC with collision-induced dissociation mass spectrometry (UHPLC-CID-MS), UHPLC-CTD-MS yielded fewer ambiguous ions and more structurally informative results.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Baptiste Moge, Baptiste Schindler, Oznur Yeni, Isabelle Compagnon
Summary: Using ion vibrational spectroscopy, researchers determine the structure and linkage of fucosylated fragments of glycans and discover a new type of fucose migration. This research provides insights into the characterization of glycans and the underlying processes in mass spectrometry.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Multidisciplinary Sciences
Parisa Bayat, Charlotte Rambaud, Bernard Priem, Matthieu Bourderioux, Melanie Bilong, Salome Poyer, Manuela Pastoriza-Gallego, Abdelghani Oukhaled, Jerome Mathe, Regis Daniel
Summary: This study demonstrates the label-free detection and analysis of glycosaminoglycan molecules using biological nanopores, reaching a high resolution in deciphering structural information. It is an important step towards the ultimate goal of glycosaminoglycan sequencing.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Applied
Jeremy Manheim, Mingxiang Lin, John Kong, Mirlinda Biba, Ping Zhuang
Summary: This study successfully differentiated and quantified isomeric pneumococcal polysaccharides using a partial chemical degradation mass spectrometry approach. The results demonstrated high precision and robustness of this method.
CARBOHYDRATE POLYMERS
(2022)
Article
Biochemical Research Methods
Yuyang Zhang, Wanru Li, Haoran Lei, Xueming Dong, Hilkka Kenttaemaa
Summary: Asphaltenes in heavy crude oil contain nitrogen-containing heteroaromatic compounds that can deactivate catalysts in refinery processes. This study developed an analytical approach using mass spectrometry to differentiate isomeric molecular radical cations of n-pentylquinoline and understand their fragmentation pathways. The results showed distinct fragmentation patterns depending on the location of the alkyl side chain in the quinoline ring, and quantum chemical calculations were used to explain the observed mechanisms. This approach will facilitate the structural characterization of nitrogen-containing heteroaromatic compounds in asphaltenes.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Chemistry, Analytical
Holly-May Lewis, Catia Costa, Veronique Dartois, Firat Kaya, Mark Chambers, Janella de Jesus, Vladimir Palitsin, Roger Webb, Melanie J. Bailey
Summary: This study combines elemental imaging and a new method for spatially resolved lipidomics to investigate the relationship between metals, drugs, and lipids in different areas of tissues. The method was applied to rabbit lung tissues with tuberculosis infection and demonstrated the association between ion accumulation, lipid profiles, and local drug distribution.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Tobias Ensslen, Kumar Sarthak, Aleksei Aksimentiev, Jan C. Behrends
Summary: The use of a protein nanopore is demonstrated to differentiate posttranslational modifications (PTMs) in proteins or peptides based on the positions of acetylated and methylated lysine residues. This method detects PTMs and their positions by sensing the shape of a fully entrapped peptide, eliminating the need for controlled translocation. This molecular shape-sensing principle offers a versatile, label-free, and high-throughput characterization of protein isoforms.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Multidisciplinary
Tsukasa Uchida, Ayano Nakamura, Hannah Shimazaki, Yoshimi Kanie, Osamu Kanie
Summary: Biosensors play an important role in diagnosis, but stability issues of receptor biomolecules limit their application. This study addresses the stability issues by utilizing small molecules presented on porous silica particles as receptor components. Carbohydrates are used as a chiral scaffold to synthesize receptor components, which are then attached to the porous silica particles. The results show that these receptor components have selective recognition ability for specific molecules.
Article
Chemistry, Medicinal
Federico Riu, Alessandro Ruda, Olof Engstrom, Claudio Muheim, Hani Mobarak, Jonas Stahle, Paul Kosma, Antonio Carta, Daniel O. Daley, Goran Widmalm
Summary: In this study, docking and molecular dynamics simulations were used to identify potential compounds from libraries A and B that can bind to WaaG. The substructure of the inner core of LPS was also investigated. The findings provide insights into the function and catalytic cycle of the enzyme WaaG.
Article
Biochemistry & Molecular Biology
Axel Furevi, Alessandro Ruda, Thibault Angles D'Ortoli, Hani Mobarak, Jonas Stahle, Christoffer Hamark, Carolina Fontana, Olof Engstrom, Patricia Apostolica, Goran Widmalm
Summary: This article introduces a method for determining the structure of carbohydrates using NMR spectroscopy and computational approaches. The CASPER program can predict H-1 and C-13 NMR chemical shifts based on chemical shift data, and the accuracy of these predictions can be improved by experimental assignment of chemical shifts. The program was used to predict chemical shifts and determine structures of oligosaccharides containing sialic acid and O-antigen polysaccharides from E. coli O174, showing good agreement between experimental and predicted data.
CARBOHYDRATE RESEARCH
(2022)
Editorial Material
Chemistry, Multidisciplinary
Tsukasa Uchida, Ayano Nakamura, Hannah Shimazaki, Yoshimi Kanie, Osamu Kanie
Summary: Biosensors are important in specific receptor-ligand interactions. However, the stability issues of receptor biomolecules can be addressed by using small molecules as receptor components. In this study, receptor components were synthesized using carbohydrates and attached to porous silica particles. Raman spectral analyses revealed specific interaction between nitrobenzene derivatives and one of the receptor components. Chiral selective recognition was also achieved.
Review
Chemistry, Medicinal
Federico Riu, Alessandro Ruda, Roberta Ibba, Simona Sestito, Ilenia Lupinu, Sandra Piras, Goran Widmalm, Antonio Carta
Summary: This article introduces the differences between gram-positive and gram-negative bacteria, discusses the structural and functional properties of cell wall polysaccharides and peptidoglycan, and explores drug treatments targeting these structures and bacterial resistance to drugs. Additionally, the use of carbohydrate-based vaccines as a preventive strategy against bacterial infections is proposed.
Article
Chemistry, Multidisciplinary
Dirk Auman, Felix Ecker, Sophie L. Mader, Kevin M. Dorst, Alois Braeuer, Goran Widmalm, Michael Groll, Ville R. I. Kaila
Summary: In this study, we combine high-resolution X-ray crystallography, enzyme engineering, quantum-classical (QM/MM) simulations, and biochemical assays to uncover the existence of a peroxidic intermediate bridging the substrate and active site metal ion in AsqJ. We also find that the homolytic cleavage of this intermediate during substrate epoxidation generates an activated high-valent ferryl (FeIV = O) species for mediating the next catalytic cycle. These combined findings provide important insights into the chemical bond activation principles and molecular mechanisms of dioxygenases in complex enzymatic reaction networks.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Review
Chemistry, Multidisciplinary
Carolina Fontana, Goran Widmalm
Summary: Glycans are important in biology and their structures, which determine their interaction with other molecules, can be resolved in greater detail using advanced NMR techniques and hardware developments.
Article
Chemistry, Medicinal
Ya Gao, Goran Widmalm, Wonpil Im
Summary: In this study, the impact of different forms of Escherichia coli extracellular capsule on the properties of LPS bilayers was investigated through molecular dynamics simulations. It was found that the presence of KLPS made the acyl chains of LPS more rigid and ordered, while the presence of KPG made them less ordered and flexible. These findings contribute to a better understanding of the biological functions of bacterial extracellular capsules and the properties of outer membranes.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Multidisciplinary
Jeahoo Kwon, Alessandro Ruda, Hugo F. Azurmendi, Jasmin Zarb, Marcos D. Battistel, Liang Liao, Ari Asnani, France-Isabelle Auzanneau, Goran Widmalm, Daron I. Freedberg
Summary: We provide evidence for nonconventional hydrogen bonding in 10 Lewis antigens and two rhamnose analogues. The thermodynamics and kinetics of these hydrogen bonds are characterized, and a plausible explanation for their presence in Lewis antigens is presented. Our findings shed light on the contribution of nonconventional hydrogen bonding to molecular structure and can be used for rational drug design.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biochemistry & Molecular Biology
Yoshimi Kanie, Yuya Maegawa, Yi Wei, Osamu Kanie
Summary: O-Linked alpha-N-acetylgalactosamine (alpha-GalNAc) in Gc protein is crucial for macrophage activation, and the GalNAc-attached form is known as Gc macrophage activating factor (GcMAF). The glycans on Gc protein are hydrolyzed by alpha-Sia-ase and beta-Gal-ase, resulting in the production of GcMAF. In this study, we investigated the protective effects of an iminocyclitol inhibitor against GcMAF by inhibiting alpha-GalNAc-ase activity. Detailed mass spectrometric analyses and tandem mass spectrometric (MS/MS) analysis were performed to study the glycosylation site and glycan structure.
Article
Biochemistry & Molecular Biology
Ryosuke Yamaguchi, Yoshimi Kanie, Takashi Kazamaki, Osamu Kanie, Yoshitaka Shimizu
Summary: Glucocerebroside (GlcCer), consisting of glucose and ceramide, has anti-tumor activity and can improve skin barrier function for atopic patients when taken orally. However, its absorption is low due to aggregation in aqueous solution, which can be improved by forming a liposome. We prepared a GlcCer-liposome with high GlcCer content and demonstrated its immediate internalization into cells without significant accumulation on the plasma membrane, suggesting its potential as a carrier for dietary and/or drug molecules.
CARBOHYDRATE RESEARCH
(2023)
Article
Biology
Benjamin Wiseman, Goeran Widmalm, Martin Hoegbom
Summary: Through cryo-electron microscopy, it was discovered that the co-polymerase WzzE, responsible for length modulation of the enterobacterial common antigen, consists of eight subunits arranged in alternating up-down conformations. The clashing helical faces between adjacent protomers contribute to the alternating arrangement of the L4 loops, creating a dynamic environment for polysaccharide elongation. This study provides insight into the mechanisms of lipopolysaccharide elongation and length regulation.
COMMUNICATIONS BIOLOGY
(2023)
Article
Chemistry, Organic
Marshall J. J. Smith, Emma L. L. Gates, Goran Widmalm, Ralph W. W. Adams, Gareth A. A. Morris, Mathias Nilsson
Summary: Human milk oligosaccharides are bioactive molecules that have diverse effects on infant development. NMR provides important structural information about these oligosaccharides, but signal overlap in the spectra makes this information difficult to obtain. This study demonstrates the benefits of combining pure shift methods with the CASPER computational approach for resonance assignment in oligosaccharides.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Axel Furevi, Jonas Stahle, Claudio Muheim, Spyridon Gkotzis, Daniel O. Daley, Klas Udekwu, Goran Widmalm
Summary: The structure of the O-antigen from the international reference strain Escherichia coli O93:-:H16 has been determined using bioinformatics information, NMR spectra, and computer program CASPER. The polysaccharide carries O-acetyl groups, with varying locations on the repeating unit. The tetrasaccharide repeating unit of the O-antigen is similar to capsular polysaccharides from other E. coli strains.
Article
Chemistry, Medicinal
Ya Gao, Goran Widmalm, Wonpil Im
Summary: Capsule is a common virulence factor in Gram-negative bacteria, providing protection to pathogens from host defenses. This study models representative Escherichia coli CPS and incorporates it into symmetric bilayers with LPS. Molecular dynamics simulations reveal that the presence of CPS affects various properties of the bilayers, such as the rigidity and order of LPS's acyl chains.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
