Article
Chemistry, Multidisciplinary
Emmanuel Sursin, Amandine. L. L. Flourat, Z. L. Evariste Akissi, Agathe Martinez, Nicolas Borie, Cedric Peyrot, Eric Courot, Jean-Marc Nuzillard, Jean-Hugues Renault, Laurence Voutquenne-Nazabadioko, Florent Allais
Summary: This study achieved high-yield bioproduction and purification of E-labruscol through enzyme-catalyzed dimerization and the application of an ionic liquid in the separation process. Furthermore, four new resveratrol dimers were identified.
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2023)
Article
Biochemistry & Molecular Biology
Maria Jose Garcia-Jimenez, Myriam Torres-Rico, Jose L. de Paz, Pedro M. Nieto
Summary: In this study, the interaction between synthetic models of CS types and mimetics with PTN was investigated using NMR techniques. The introduction of lipophilic substituents in the ligand structure was found to improve the binding strength of PTN, and the binding modes of PTN and MK were similar with multiple binding modes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Spectroscopy
Chengqian Huo, Guiliang Liu, Mengchen Xu, Xiangxiang Li, Wansong Zong, Rutao Liu
Summary: This study investigated the interaction mechanism between food additives and antioxidant enzymes, focusing on the effect of sodium benzoate on the structure and function of lysozyme at the molecular level. The results showed that sodium benzoate statically quenched the intrinsic fluorescence of lysozyme, formed complexes with lysozyme through hydrophobic interaction and hydrogen bond, and increased lysozyme activity. The study provides experimental support for evaluating the edible safety of sodium benzoate.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2021)
Review
Biochemistry & Molecular Biology
Kenichi Kasai
Summary: Frontal affinity chromatography (FAC) is a versatile research method that overcomes inherent difficulties to provide accurate information on weak interactions, with great potential to solve difficult problems in general bioscience.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2021)
Article
Biochemical Research Methods
Luis Alberto Menjia-Manzano, Victor R. Campos-Garcia, Francisco C. Perdomo-Abundez, Emilio Medina-Rivero, Jose Gonzalez-Valdez
Summary: This study presents a novel method for the purification of PEGylated proteins using a modified heparin-affinity monolith disk. The results demonstrate that this method offers high purity and productivity, with improved efficiency compared to traditional methods.
JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES
(2022)
Article
Chemistry, Physical
Na Li, Ying Wang, Leping Dang, Bo Zhang, Zhanzhong Wang
Summary: In this study, the effects of four hydrophilic ionic liquids (ILs) on lysozyme activity and molecular interaction in aqueous solutions were investigated. The results showed that the effect of ILs on lysozyme activity depended on their concentration. ILs exhibited a quenching effect on the fluorescence of lysozyme, and this effect increased with increasing ILs concentration. The conformational changes of lysozyme triggered by changes in the microenvironment surrounding Trp62 or Trp108 were found to be responsible for the effects of ILs on lysozyme activity.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Chemistry, Multidisciplinary
Hiroaki Tatsuoka, Takumi Yamaguchi
Summary: Interaction with water molecules plays a role in regulating carbohydrate functions. NMR measurements were conducted to analyze the effects of three methyl sugars on water in solution. The proton exchange between carbohydrates and water, as well as between water molecules, was studied using H2O/D2O and dimethylsulfoxide mixed solvents. 13C NMR analysis revealed slower carbohydrate-water proton exchange in the mannose solution compared to others, and frequent proton exchange between waters was observed in the mannose solution. These findings highlight the importance of solvation environments and geometric characteristics of carbohydrates.
BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN
(2023)
Article
Engineering, Chemical
Wei Gao, Feng Zhang, Sen Zhang, Jia-yuan Li, Hong-zhen Lian
Summary: High selective enrichment of low abundance phosphopeptides from complex biological samples is essential for in-depth phosphoproteomics. A magnetic material called mMOF-FBP-Ti4+, fabricated by grafting UiO-66-NH2 metal-organic framework onto the surface of Fe3O4 and immobilizing Ti(IV) with fructose 1,6-bisphosphate, exhibited favorable properties for phosphopeptide enrichment. The material demonstrated strong affinities through metal oxide affinity chromatography and immobilized metal affinity chromatography, as well as improved hydrophilicity for enhanced hydrophilic chromatography interaction. The mMOF-FBP-Ti4+ also yielded low detection limit, high selectivity, good reusability, and high postenrichment recovery towards phosphopeptides, making it a promising tool for efficient enrichment in complex biological samples.
SEPARATION AND PURIFICATION TECHNOLOGY
(2023)
Article
Chemistry, Analytical
Csenge Lilla Szabo, Fanni Sebak, Andrea Bodor
Summary: Protein unfolding and denaturation are important issues in biochemical and pharmaceutical research. This study provides a method to distinguish folded, unfolded, and intrinsically disordered proteins based on their distinct hydrodynamic properties. By using a global parameter called the translational diffusion coefficient D, the molecular mass and folding degree of proteins can be accurately determined. The study also investigates the effect of different solvents on protein structure.
ANALYTICAL CHEMISTRY
(2022)
Review
Chemistry, Analytical
Clara Davoine, Lionel Pochet, Marianne Fillet
Summary: Detection and characterization of biomolecular interactions are crucial for drug discovery. Fragment-based drug discovery (FBDD) is a widely used approach to discovering new drugs. However, it can be challenging to execute FBDD due to the difficulty of discovering weak binders and determining their growth or binding. This article comprehensively reviews emerging analytical technologies in FBDD compared with conventional ones, providing examples and insights for the selection and implementation of an analytical platform for FBDD projects.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Chae Hwan Cho, Se-Young Son, Jeong Kyu Bang, Young Ho Jeon, Jong Pil Park
Summary: Allergy-causing inflammatory diseases have become a global health problem. This study identified specific peptides that bind to IL-33 and described their molecular interactions. The peptide with the highest binding affinity was identified as FGLEPRANLHFT. The study also investigated the primary peptide binding site of IL-33 and suggested potential applications in drug development and allergy diagnosis.
ANALYTICA CHIMICA ACTA
(2022)
Article
Energy & Fuels
Saroj K. Panda, Donya A. Alsewdan, Munther M. Alshammari, Qasim Saleem, Dominic J. Kearney
Summary: Aromatics in petroleum mixtures are important in various aspects including exploration, refining, and environmental emissions. This study presents a simple and fast method called aromatic-selective size exclusion chromatography (ASSEC) for quantifying aromatics in petroleum samples. ASSEC can provide a comprehensive analysis of aromatics content across the whole boiling range of petroleum samples and can be used for industrial applications such as optimizing conversions of petroleum to petrochemicals. Further optimization can reduce differences between ASSEC and other analytical techniques for determining aromatic content.
Article
Chemistry, Multidisciplinary
Carina Lemke, Adela Jilkova, Dominic Ferber, Annett Braune, Anja On, Patrick Johe, Alena Zikova, Tanja Schirmeister, Michael Mares, Martin Horn, Michael Gutschow
Summary: We developed a bimodal rhodesain probe that can detect and quantify rhodesain with high sensitivity, and used it for inhibitor screening. This probe provides a new tool for studying Trypanosoma pathobiochemistry and antitrypanosomal drug discovery.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Chemistry, Analytical
Jean Rouillon, Caroline Arnoux, Cyrille Monnereau
Summary: This study introduces a new method for determining the absolute photoinduced radical generation efficiency via NMR monitoring, relying on a radical scavenger probe with a nitroxide moiety and a trifluoromethyl group. The method showed good agreement with literature values, proving its robustness, and highlighted its potential for quantitative determination of photoinduced radical generation efficiency.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Applied
O. N. Makshakova, L. R. Bogdanova, D. A. Faizullin, E. A. Ermakova, Yu. F. Zuev, I. A. Sedov
Summary: The study shows that x-carrageenan can form insoluble complexes with lysozyme, adopting different conformations at different concentrations. It has a preference for regions rich in 8-structures in the protein. This interaction could be useful in developing carrageenan-based protection against amyloid-like protein aggregation.
CARBOHYDRATE POLYMERS
(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)
Article
Food Science & Technology
Jiyun Liu, Mohammed E. Hefni, Cornelia M. Witthoft, Maria Bergstrom, Stephen Burleigh, Margareta Nyman, Frida Hallenius
Summary: This study found that the flavonoids and dietary fiber in lingonberries have different effects on atherosclerotic plaques, gut microbiota, and metabolites.
INTERNATIONAL JOURNAL OF FOOD SCIENCES AND NUTRITION
(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).
Article
Chemistry, Organic
Faiza Diaba, Gisela Trenchs
Summary: The first violet light-mediated synthesis of gamma- and delta-lactams from N-alkenyl trichloroacetamides is reported in this paper. The reactions are conducted in tetrahydrofuran or 2-methyltetrahydrofuran as the sole solvent without catalysts or additives, under non-anhydrous conditions in an air atmosphere where the solvent serves as the radical initiator.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2024)
Article
Chemistry, Organic
Feroze Hussain, Sajjad Ahmed, Ashiq Hussain Padder, Qazi Naveed Ahmed
Summary: This study reports a novel and efficient one-pot synthesis method for mixed phosphorotrithioates, which does not require supplementary additives and shows broad applicability.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2024)
Article
Chemistry, Organic
Hyunjin Oh, Ikyon Kim
Summary: A new 1,2,4-triazole-pyrrolo[1,2-a]pyrazine hybrid system, 6-acylpyrrolo[1,2-a][1,2,4]triazolo[5,1-c]pyrazine, was synthesized using a catalyst-free method. This method involved sequential exposure of pyrrole-2-carbonitrile-derived substrates to DMF-DMA and acyl hydrazide, resulting in the formation of acylated pyrazine and 1,2,4-triazole rings, enabling the installation of various substituents at specific positions on the core skeleton.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2024)
Article
Chemistry, Organic
Ming Yan, Si-fan Wang, Yong-po Zhang, Jin-zhong Zhao, Zhuo Tang, Guang-xun Li
Summary: Here we developed an efficient photocatalytic approach for the convenient preparation of sulfinamides. The reaction allows for the gram-scale preparation of sulfinamides and the one-pot synthesis of various sulfonyl amides.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2024)
Article
Chemistry, Organic
Farzaneh Bandehali-Naeini, Zahra Tanbakouchian, Noushin Farajinia-Lehi, Nicolas Mayer, Morteza Shiri, Martin Breugst
Summary: Two tandem catalytic systems were developed for the synthesis of novel 3,4-disubstituted maleimides using the same Ugi adducts. Different maleimide structures can be synthesized using either Pd or Cu catalysis.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2024)
Article
Chemistry, Organic
Tanya Raghava, Anjan Chattopadhyay, Subhadeep Banerjee, Nivedita Sarkar
Summary: Amine substitution of two ortho fluorine atoms of tetrafluoroterephthalonitrile through SNAr chemistry is easily achievable. But further fluorine substitution is only possible under forcing conditions, yielding valuable fluorophores for bioimaging.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2024)
Review
Chemistry, Organic
Anju Chadha, Santosh Kumar Padhi, Selvaraj Stella, Sowmyalakshmi Venkataraman, Thangavelu Saravanan
Summary: Alcohol dehydrogenases are enzymes that use cofactors for oxidation or reduction reactions of alcohols or carbonyl compounds. They are utilized in green chemistry and have applications in the production of pharmaceuticals. Recombinant enzymes have solved the challenge of producing purified enzymes in large quantities. Engineered alcohol dehydrogenases have been used in asymmetric synthesis in industry. Various methods have been established for regenerating expensive cofactors to make the enzymatic process more efficient and economically viable.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2024)