Article
Chemistry, Multidisciplinary
Oscar Francesconi, Francesco Milanesi, Cristina Nativi, Stefano Roelens
Summary: In designing new biomimetic receptors for carbohydrates, shape-persistent macrocyclic structures are commonly chosen for effective recognition of neutral saccharides in water. However, this study found that acyclic receptors, while less explored, provide advantages in terms of selectivity for recognizing important 1,4-disaccharides in biological contexts. NMR spectroscopic data and molecular modeling calculations were used to analyze the differences in binding mode and shed light on the origin of recognition efficacy and selectivity.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Chemistry, Physical
Hao Wang, Walther Caminati, Meng Li, Junhua Chen, Xiao Tian, Jens-Uwe Grabow, Qian Gou
Summary: This study uses high-resolution rotational spectroscopy to observe and characterize two isomers of the acrolein dimer. The first isomer is stabilized by hydrogen bonds and has a planar configuration, while the second isomer exhibits unique interactions and tunneling motion.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Physical
Hao Wang, Walther Caminati, Meng Li, Junhua Chen, Xiao Tian, Jens-Uwe Grabow, Qian Gou
Summary: In this study, two isomers of acrolein dimer were observed and characterized using high-resolution rotational spectroscopy in pulsed jets. The first isomer, stabilized by two hydrogen bonds, exhibits a planar configuration and is energetically favored over the second isomer. Surprisingly, the study reveals that the second isomer, with a dominant n -> pi* interaction, enables a concerted tunneling motion along the carbonyl group. This motion leads to the inversion of transient chirality associated with the exchange of donor-acceptor roles.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Multidisciplinary
Oliver Loveday, Jorge Echeverria
Summary: The study explores a novel hydrogen bond where a methyl group, bound to an electropositive atom, acts as the acceptor through its carbon atom. Experimental examples from the Cambridge Structural Database show a trend towards a linear arrangement of interacting groups as the interatomic distance decreases. Computational techniques were used to investigate the strength and nature of the hydrogen bond, revealing charge transfer from a sigma(E-C) bonding orbital of the methyl group to a sigma* antibonding H-Y orbital.
CRYSTAL GROWTH & DESIGN
(2021)
Article
Chemistry, Multidisciplinary
Junki Ochi, Kazuhiro Yuhara, Kazuo Tanaka, Yoshiki Chujo
Summary: Researchers demonstrated solid-state dual-emissive o-carborane derivatives, in which the dual-emission intensity ratios were changed by regulating intra-molecular interactions, and the overall photoluminescence spectra were estimated using the binding energy of intra-molecular interactions.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Chemistry, Analytical
Amanda Helms, Edwin E. E. Escobar, Saulius Vainauskas, Christopher H. H. Taron, Jennifer S. S. Brodbelt
Summary: The complete characterization of O-glycopeptides, including identification of peptides, localization of glycosites, and mapping of glycans, has been a challenging task in O-glycoproteomics. This study successfully applied a strategy combining the use of O-glycoprotease IMPa and HCD-triggered UVPD to achieve the complete characterization of O-glycopeptides. This approach allowed the localization of multiple adjacent or proximal O-glycosites and the identification of a previously unknown glycosite on etanercept.
ANALYTICAL CHEMISTRY
(2023)
Article
Energy & Fuels
Chengzhe Gao, S. Sherry Zhu, Marta Antoniv, Gawain Thomas
Summary: Tracers, or markers, are widely used in subsurface and environmental monitoring. This study presents the development of the first generation of transient markers that perform their marker function for a short period of time before degrading to undetectable molecules in the environment. These markers show potential for applications in subsurface environments, such as reservoir management, interwell monitoring, and obtaining lithological information.
Article
Chemistry, Multidisciplinary
Supriya Rej, Naoto Chatani
Summary: Organoboron reagents play a crucial role in synthetic organic chemistry, and current selective borylation strategies rely heavily on transition-metal catalysts. However, this study introduces a transition-metal-free approach for selective C-H borylation of electron-deficient benzaldehyde derivatives, demonstrating effectiveness even in the presence of external impurities.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Multidisciplinary Sciences
Ken Chen, Qingrui Zeng, Longhuan Xie, Zisheng Xue, Jianbo Wang, Yan Xu
Summary: In this study, a photocatalytic reversible C-H sampling reaction was developed to achieve the translocation of cyano groups in nitriles. This reaction enables the direct exchange between a cyano group and an unactivated C-H bond, offering a selective and valuable method for the synthesis of unconventional C-H derivatives and building blocks of bioactive molecules.
Article
Chemistry, Multidisciplinary
Ruder Susanj, Vinko Nemec, Nikola Bedekovic, Dominik Cincic
Summary: In this study, the halogen bond acceptor potential of oxygen and nitrogen atoms in morpholine and piperazine fragments were investigated. Four acceptor molecules derived from acetylacetone or benzoylacetone were synthesized, and co-crystallized with 1,4-diiodotetrafluorobenzene and 1,3,5-triiodotrifluorobenzene. The results showed the formation of halogen bonds with the oxygen atom of the morpholine fragment and the nitrogen atom of the piperazine fragment. The acceptor sites of nitrogen and oxygen atoms were evaluated through calculations of molecular electrostatic potential values.
CRYSTAL GROWTH & DESIGN
(2022)
Article
Multidisciplinary Sciences
Oliver Loveday, Jorge Echeverria
Summary: Under certain conditions, methyl groups can act as electron density donors in noncovalent interactions, contrary to their usual role as electron density acceptors. Thousands of experimental structures demonstrate the ability of methyl groups to participate in various types of bonds with different elements.
NATURE COMMUNICATIONS
(2021)
Article
Agriculture, Multidisciplinary
Haiyan Wang, Ximei Zhang, Peng Kang, Xiuxiu Cui, Guo Hao, Zhongfu Wang, Bei Han, Xin Lv, Jing Zhang, Wupeng Ge
Summary: Oligosaccharides and N/O-glycans are abundant in human milk, with variations observed during lactation. Colostrum has the highest levels of oligosaccharides, which decrease as lactation progresses. Sialylated oligosaccharides and N/O-glycans are highly abundant in colostrum.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Chemistry, Analytical
Miyang Li, Ting-jia Gu, Xiaorong Lin, Lingjun Li
Summary: Glycosylation plays a key role in physiological functions, but high-throughput quantitative analysis of O-glycans has been overlooked. A multiplexed isobaric labeling method has been introduced to release and label O-glycans in a single reaction, enabling the processing of four samples simultaneously for accurate relative quantification.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Applied
Mostafa Akhlaghi Bagherjeri, Hassan Monhemi, Abu Naser Md Ahsanul Haque, Maryam Naebe
Summary: In this study, the complete dissolution process of cellulose in NMMO monohydrate and EmimAc was simulated using molecular dynamic simulations. It was found that cellulose can be completely and efficiently dissolved in both solvents. The dissolution time of cellulose in NMMO monohydrate was almost twice that in EmimAc. Although hydrogen bonding was identified as the main driving force for cellulose dissolution in NMMO monohydrate, it was proposed that the interactions between NMMO molecules, rather than with cellulose, play a critical role in the dissolution process.
CARBOHYDRATE POLYMERS
(2024)
Article
Chemistry, Multidisciplinary
Jialin Liu, Bo Cheng, Xinqi Fan, Xinyue Zhou, Jiankun Wang, Wen Zhou, Hengyu Li, Wenfeng Zeng, Pengyuan Yang, Xing Chen
Summary: Proteins are extensively modified with glycans of different structures, making it challenging to map the protein glycosylation landscape. This study presents Click-iG, a method that enables the simultaneous enrichment and profiling of three types of intact glycopeptides using metabolic labeling of glycans, optimized mass spectrometry, and tailored software analysis. Click-iG was able to identify thousands of intact glycosites in cell lines and living mice, providing comprehensive coverage of the protein glycosylation landscape and laying the foundation for investigating crosstalk between different glycosylation pathways.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Multidisciplinary Sciences
Benjamin Wiseman, Ram Gopal Nitharwal, Goeran Widmalm, Martin Hogbom
Summary: Lipopolysaccharides, crucial components of bacterial cell envelopes, are synthesized at the inner membrane through the Wzx/Wzy-dependent assembly pathway. The cryo-EM structure of intact E. coli WzzB provides insights into the transmembrane and cytoplasmic domains, as well as a conserved proline-rich segment near the C-terminal transmembrane helix.
NATURE COMMUNICATIONS
(2021)
Article
Plant Sciences
Erwan Chavonet, Matthieu Gaucher, Romain Warneys, Antoine Bodelot, Christelle Heintz, Anthony Juillard, Raphael Cournol, Goran Widmalm, Joanna K. Bowen, Cyril Hamiaux, Marie-Noelle Brisset, Alexandre Degrave
Summary: This study identifies and characterizes a class of apple PR proteins called MdAGGs, which are abundantly produced in leaf tissues and correspond to enhanced resistance to E. amylovora. The study also reveals that E. amylovora represses the expression of MdAGG genes by injecting an effector and secreting bacterial exopolysaccharides. Furthermore, the study demonstrates that MdAGG protein can agglutinate E. amylovora cells and bind bacterial lipopolysaccharides in vitro.
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)
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
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)
Article
Biochemistry & Molecular Biology
Axel Furevi, Klas Udekwu, Goran Widmalm
Summary: This study elucidates the structure of the O-antigen polysaccharide from Enteropathogenic Escherichia coli O125ac:H6 through NMR experiments and sugar analysis, confirming a branched pentasaccharide structure for the repeating unit. Additionally, by utilizing the CASPER program, the O-antigen structure of O125ab, composed of hexasaccharide repeating units, was established in a semi-automated manner. The close similarity between the O-antigen structures supports the presence of two subgroups within the E. coli O125 serogroup.
Article
Chemistry, Multidisciplinary
Jin-Min Shi, Ting-Ting Wu, Hui Zhou, Yao-Yao Zhang, Li Liu, Goran Widmalm, Josef Voglmeir
Summary: Galactokinases (GalKs) are a group of structurally conserved proteins found in all life forms. A unique GalK orthologue from the bacterium Solitalea canadensis (ScGalK) has been discovered with relaxed substrate requirements and the ability to convert xylose to xylose-1-phosphate. Further investigation identified a putative Glucose-1-phosphate Uridyltransferase (ScGPUT) in close proximity to the ScGalK gene, which can convert xylose-1-phosphate to uridine diphosphate xylose (UDP-xylose) with the presence of uridine triphosphate (UTP).