Article
Chemistry, Multidisciplinary
Thorben Maass, George Ssebyatika, Marlene Brueckner, Lea Breckwoldt, Thomas Krey, Alvaro Mallagaray, Thomas Peters, Martin Frank, Robert Creutznacher
Summary: This study used NMR experiments to investigate the binding of selected glycans and glycomimetics to the SARS CoV-2 spike glycoprotein and its receptor binding domain. The results revealed strong binding between sialoglycans and the Wuhan strain S-protein, weak binding between sialoglycans and the Omicron/BA.1 S-protein, and no binding between sialoglycans and the Delta 143-145 deletion mutant of the Wuhan S-protein. Additionally, the glycomimetics Oseltamivir and Zanamivir exhibited weak binding to the S-protein of both virus strains.
CHEMISTRY-A EUROPEAN JOURNAL
(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
Chemistry, Physical
Jiandu Hu, Jihyun Kim, Christian Hilty
Summary: The transfer of nuclear spin hyperpolarization from water to ligand F-19 spins can be used to detect protein-ligand interaction without background noise. The calculated cross-relaxation rates indicate that these rates are sensitive to binding to medium- and large-sized proteins. The heteronuclear observation of hyperpolarization transfer from water can be applied in screening protein-ligand interactions in drug discovery and other applications.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Materials Science, Paper & Wood
Martin Nagl, Oskar Haske-Cornelius, Lukas Skopek, Florian Bausch, Alessandro Pellis, Wolfgang Bauer, Gibson S. Nyanhongo, Georg M. Guebitz
Summary: Endoglucanases are potential solutions for reducing energy consumption in the pulp and paper industry, but the performance varies due to the different enzyme formulations. This study investigated the effect of four endoglucanases on softwood and hardwood pulp, revealing that degradation of amorphous regions is beneficial for the refining process.
Article
Multidisciplinary Sciences
Noriko Suzuki, Tatsuya Abe, Shunji Natsuka
Summary: This study analyzed N-glycan structures in chicken respiratory tracts and found that avian influenza A viruses preferentially bind to glycans with Sia alpha 2-3Gal. The results showed that chicken trachea had a high abundance of fucosylated alpha 2,3-Sia, while no fucosylation was detected in the lung. Additionally, lung tissue contained a small amount of N-glycans with 6-sulfo sialyl LacNAc. These findings suggest that avian influenza A viruses do not evolve to bind to alpha 2,6-Sia, regardless of its abundance.
SCIENTIFIC REPORTS
(2022)
Article
Chemistry, Multidisciplinary
Philipp Schlee, Dmitry Tarasov, Davide Rigo, Mikhail Balakshin
Summary: Our AqSO process has potential as a parameter-controlled biorefinery, allowing for tailored lignin products. We characterized the structure of AqSO lignins using NMR and investigated the effects of process severity and liquid-to-solid ratio. Lower severity and L/S=1 led to less degraded lignin with higher β-O-4 content, while harsher conditions yielded more condensed lignins. We identified and quantified new lignin moieties and hypothesized the formation of lignin carbohydrate complexes at low severity and L/S.
Article
Chemistry, Applied
Qi Shi, Jingyu Yan, Bin Jiang, Xiujuan Chi, Jihui Wang, Xinmiao Liang, Xuanjun Ai
Summary: The study explored a strategy for carbohydrate structural determination using combined multi-dimensional spectroscopies, which was successfully applied to simplify data analysis and determine residue connections for complex structures. The potential of this technique for structural determination of complex polysaccharides was demonstrated through the analysis of chondroitin sulfate from bovine cartilage.
CARBOHYDRATE POLYMERS
(2021)
Article
Multidisciplinary Sciences
Markus Hackl, Edward V. Contrada, Jonathan E. Ash, Atharv Kulkarni, Jinho Yoon, Hyeon-Yeol Cho, Ki-Bum Lee, John M. Yarbrough, Cesar A. Lopez, Sandrasegaram Gnanakaran, Shishir P. S. Chundawat
Summary: Protein adsorption to solid carbohydrate interfaces is crucial in biological processes such as biomass deconstruction. This study focuses on understanding the interactions between carbohydrate-binding modules (CBMs) and polysaccharides to improve enzymatic efficiency in biomass deconstruction. The research presents a method using single-molecule force spectroscopy to study the unbinding behavior of CBMs from polysaccharide surfaces. The results reveal distinct CBM binding conformations and provide insights into the structural mechanisms through molecular dynamics simulations.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Engineering, Environmental
Z. Z. Mustafa, N. R. H. Rao, G. Johnston-Hall, R. K. Henderson, G. L. Leslie, P. Le-Clech
Summary: Extracellular organic matter released by algae during algal blooms presents challenges for ultrafiltration fouling management. This study investigates the impact of biopolymer interactions and membrane surface properties on fouling behavior, providing insights for more effective UF management.
JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING
(2022)
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
Chemistry, Physical
Li Han, Haipeng Wang, Wensheng Cai, Xueguang Shao
Summary: The molecular mechanism of how polyproline inhibits ice growth and exhibits antifreeze activity was investigated through spectroscopy and molecular dynamics simulations. The results demonstrate that high concentrations of PPro inhibit ice growth by weakening the interfacial water between the ice crystal and hydrophobic groups of PPro.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Physical
Li Han, Haipeng Wang, Wensheng Cai, Xueguang Shao
Summary: The study investigated the change in the structure of water during ice growth in polyproline (PPro) solutions using near-infrared spectroscopy and molecular dynamics simulations. The results show that only high concentrations of PPro solutions can effectively inhibit ice growth. When PPro exhibits an antifreeze effect, the spectral intensity of hydrated water associated with PPro in a solution is weakened. The experiments and simulations reveal the critical role of interfacial water in the antifreeze activity of PPro.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Agricultural Engineering
Xiaoxue Zhao, Caoxing Huang, Wenqian Lin, Bin Bian, Chenhuan Lai, Zhe Ling, Qiang Yong
Summary: This study investigated the adsorption mechanism and structure-activity relationship between lignin and different cellulase domains using fluorescence spectroscopy and SDS-PAGE. It was found that endo-cellulase 6B had a higher affinity to lignin fractions, which was positively correlated to molecular weight. The adsorption between lignin fractions and endo-cellulase 6B was mainly driven by van der Waals and electrostatic forces, while hydrophobic force drove the adsorption of lignin fractions to CBM4A. The results demonstrated the critical role of lignin's structure in its adsorption with various cellulase domains.
BIORESOURCE TECHNOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Elena Shanina, Sakonwan Kuhaudomlarp, Kanhaya Lal, Peter H. Seeberger, Anne Imberty, Christoph Rademacher
Summary: Carbohydrate-binding proteins, specifically lectins, are promising targets in drug discovery for combating antimicrobial resistance, yet non-carbohydrate drug-like inhibitors are still lacking. A druggable pocket in a beta-propeller lectin from Burkholderia ambifaria has been identified as a potential target for allosteric inhibitors. Future drug-discovery efforts focusing on small molecule inhibitors could benefit from targeting allosteric sites in lectins to combat antibiotic-resistant pathogens.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Biochemistry & Molecular Biology
Paul G. Kremer, Adam W. Barb
Summary: Fc gamma receptor IIIa/CD16a is a crucial receptor involved in regulating cellular immune responses. Genetic polymorphism and N-glycan composition of CD16a can affect its binding affinity and kinetics with antibodies, thus impacting immune responses and therapeutic efficacy of antibodies.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Review
Biochemistry & Molecular Biology
Francisco Javier Canada, Angeles Canales, Pablo Valverde, Beatriz Fernandez de Toro, Monica Martinez-Orts, Paola Oquist Phillips, Amaia Pereda
Summary: Carbohydrates, either as free molecules or conjugated with other biomolecules, play important roles in various biological processes. Nuclear Magnetic Resonance spectroscopy (NMR) is a versatile tool for studying the structures and interactions of carbohydrates, providing information about their sequences, structures, and local geometries. Labeling carbohydrates with 13C enhances the resolution and detail of the analyzed structures. Moreover, combining NMR with molecular modeling and theoretical calculations offers insights into the conformational flexibility of carbohydrates. Additionally, the use of partially oriented media or paramagnetic perturbations allows for the study of longer and branched glycan chains. This review presents examples and an overview of recent and relevant NMR applications in the field of glycobiology.
CURRENT MEDICINAL CHEMISTRY
(2022)
Article
Chemistry, Physical
Reyes Nunez-Franco, Gonzalo Jimenez-Oses, Jesus Jimenez-Barbero, Francisca Cabrera-Escribano, Antonio Franconetti
Summary: A multidisciplinary study is conducted to investigate the pi-pi interactions established by pyrylium frameworks as pi-hole donors. The combination of CSD analysis, computational modelling, and experimental NMR spectroscopy data provides essential information on the key parameters characterizing these interactions, paving the way for further applications of this versatile heterocycle.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Multidisciplinary
Francesco Milanesi, Luca Unione, Ana Arda, Cristina Nativi, Jesus Jimenez-Barbero, Stefano Roelens, Oscar Francesconi
Summary: Glycomics research has revealed the essential role of carbohydrates in biological systems and the importance of chemical tools in studying glycan function. While biomimetic receptors can selectively bind to simple saccharides, this study demonstrates the unprecedented recognition of a complex glycopeptide by a biomimetic receptor. The receptor shows high affinity for the core disaccharide of the N-glycan and has the potential for versatile applications in glycoscience.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Chemistry, Multidisciplinary
Marta G. Lete, Antonio Franconetti, Sara Bertuzzi, Sandra Delgado, Mikel Azkargorta, Felix Elortza, Oscar Millet, Gonzalo Jimenez-Oses, Ana Arda, Jesus Jimenez-Barbero
Summary: Fluorine (F-19) incorporation into lectins has allowed monitoring of carbohydrate binding through NMR spectroscopy. Galectin-3 (Gal3) and Galectin-8 (Gal8) with one and two carbohydrate recognition domains (CRDs), respectively, were chosen. The presence of fluorine did not significantly affect glycan binding affinity, and allowed differentiation of binding events at different sites within the same lectin.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Ana Pozo-Rodriguez, Juan A. A. Mendez-Liter, Rocio Garcia-Villalba, David Beltran, Eva Calvino, Andres G. Santana, Laura I. I. De Eugenio, Francisco Javier Canada, Alicia Prieto, Jorge Barriuso, Francisco A. A. Tomas-Barberan, Maria Jesus Martinez
Summary: Resveratrol was glycosylated by using rXynSOS-E236G glycosynthase, resulting in the production of 3-O-beta-D-xylobiosyl resveratrol as the major product. Response surface methodology was used to optimize the reaction, yielding 35% of 3-O-beta-D-xylobiosyl resveratrol. Xylobiosylation decreased the antioxidant capacity of resveratrol, but significantly improved its solubility for improved delivery and transit to the colon.
Article
Nanoscience & Nanotechnology
Anna Blasi-Romero, Molly Angstrom, Antonio Franconetti, Taj Muhammad, Jesus Jimenez-Barbero, Ulf Goransson, Carlos Palo-Nieto, Natalia Ferraz
Summary: This study combines the wound-healing properties of KR-12 peptide with wood-derived cellulose nanofibrils (CNFs) to create bioactive materials for treating chronic wounds. Different coupling chemistries were used to covalently attach KR-12 derivatives onto CNFs, and the bioactivity of KR12-CNF conjugates was evaluated in terms of antibacterial activities and anti-inflammatory effects. The results showed that thiol-ene chemistry produced the most bioactive conjugates, attributed to favorable peptide conformation and accessibility. This study advances the development of CNF-based materials for chronic wound care and provides insights into the effect of conjugation chemistry on the bioactivity of host defense peptides.
ACS APPLIED MATERIALS & INTERFACES
(2023)
Article
Chemistry, Multidisciplinary
Zhen Wang, Ana Poveda, Qingju Zhang, Luca Unione, Herman S. Overkleeft, Gijsbert A. van der Marel, Jimenez-Barbero Jesus, Jeroen D. C. Codee
Summary: Researchers have successfully synthesized a series of polysaccharide fragments with a unique structure that can activate T cells and bind to specific receptors. Detailed structural studies have revealed the secondary structure of these fragments, providing a basis for further understanding their mode of action.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Organic
Matteo A. . Tallarida, Fabrizio Olivito, Claudio D. Navo, Vincenzo Algieri, Antonio Jiritano, Paola Costanzo, Ana Poveda, Maria J. Moure, Jesus Jimenez-Barbero, Loredana Maiuolo, Gonzalo Jimenez-Oses, Antonio De Nino
Summary: The synthesis of polysubstituted spirocyclopropyl oxindoles using rare-earth metal (REM) salts, particularly Sc(OTf)3, was achieved with high diastereoselectivity (<= 94:6:0:0) in a multicomponent reaction. Density functional theory calculations on the model reaction confirmed the observed selectivity and demonstrated that the coordinating capabilities and oxophilicity of the metal played a crucial role in inducing the formation of one main diastereoisomer.
Article
Biochemistry & Molecular Biology
Hans-Christian Siebert, Thomas Eckert, Anirban Bhunia, Nele Klatte, Marzieh Mohri, Simone Siebert, Anna Kozarova, John W. Hudson, Ruiyan Zhang, Ning Zhang, Lan Li, Konstantinos Gousias, Dimitrios Kanakis, Mingdi Yan, Jesus Jimenez-Barbero, Tibor Kozar, Nikolay E. Nifantiev, Christian Vollmer, Timo Brandenburger, Detlef Kindgen-Milles, Thomas Haak, Athanasios K. Petridis
Summary: The global outbreak of SARS-CoV-2/COVID-19 has provided an opportunity and challenge to accumulate a large amount of biomedical data and test new concepts and strategies to combat the pandemic. This study correlated clinical biomedical data with structural biology and biophysical data to evaluate new diagnostic and therapeutic approaches against SARS-CoV-2. The methods used were effective in identifying potential peptide sequences and carbohydrate moieties to protect the blood-brain barrier and develop new therapeutic approaches against long-COVID symptoms.
Article
Chemistry, Multidisciplinary
Angeles Canales, Javier Sastre, Jose M. Orduna, Cindy M. Spruit, Javier Perez-Castells, Gema Dominguez, Kim M. Bouwman, Roosmarijn van der Woude, Francisco Javier Canada, Corwin M. Nycholat, James C. Paulson, Geert-Jan Boons, Jesus Jimenez-Barbero, Robert P. de Vries
Summary: Influenza virus infection remains a threat to human health due to the drifting of viral hemagglutinins, which evade infection and vaccine-induced antibody responses. Recent H3N2 and pandemic H1 viruses specifically recognize glycan structures containing at least three N-acetyllactosamine units. This study characterizes the glycan specificity of H1 variants, including the one responsible for the 2009 pandemic outbreak, and investigates the preference for tri-LacNAc motifs in human-type receptor-adapted viruses using glycan arrays, tissue binding analyses, and nuclear magnetic resonance experiments.
Article
Chemistry, Multidisciplinary
Giulio Fittolani, Theodore Tyrikos-Ergas, Ana Poveda, Yang Yu, Nishu Yadav, Peter H. Seeberger, Jesus Jimenez-Barbero, Martina Delbianco
Summary: This article introduces a synthetic glycan molecule that adopts a stable secondary structure not found in nature, called a glycan hairpin. The synthetic glycan is created by combining natural glycan motifs and utilizing unconventional hydrogen bonds and hydrophobic interactions. Nuclear magnetic resonance conformational analysis and long-range inter-residue nuclear Overhauser effects confirm the folded conformation of the synthetic glycan hairpin. The ability to control the 3D shape of glycans has the potential to provide more foldamer scaffolds with programmable properties and functions.
Review
Chemistry, Multidisciplinary
Jon I. Quintana, Unai Atxabal, Luca Unione, Ana Arda, Jesus Jimenez-Barbero
Summary: Nuclear Magnetic Resonance (NMR) is widely used to study glycan-protein molecular recognition events, providing qualitative and quantitative information at different levels of resolution and complexity. However, the weak affinity of lectin-sugar interactions is overcome by multivalency in biological processes. The application of NMR methods to monitor multivalent lectin-glycan interactions is challenging due to the disappearance of NMR signals when large macromolecular complexes are formed.
CHEMICAL SOCIETY REVIEWS
(2023)
Article
Chemistry, Multidisciplinary
Carlo Pifferi, Leire Aguinagalde, Ane Ruiz-de-Angulo, Nagore Sacristan, Priscila Tonon Baschirotto, Ana Poveda, Jesus Jimenez-Barbero, Juan Anguita, Alberto Fernandez-Tejada
Summary: The overexpression of aberrantly glycosylated tumor-associated mucin-1 (TA-MUC1) in human cancers makes it a major target for the development of anticancer vaccines derived from synthetic MUC1-(glyco)peptide antigens. However, glycopeptide-based subunit vaccines are weakly immunogenic, requiring adjuvants and/or additional immunopotentiating approaches to generate optimal immune responses.
Article
Immunology
Leticia Martin-Cruz, Marcos Vinuela, Ioanna Kalograiaki, Alba Angelina, Paola Oquist-Phillips, Irene Real-Arevalo, Francisco Javier Canada, Jose Ignacio Tudela, Luis Molto, Jesus Moreno-Sierra, Jose Luis Subiza, Oscar Palomares
Summary: This study reveals novel molecular mechanisms by which heparan sulfate-related structures associated with tumor cells promote the generation of functional Tregs in cancer. Furthermore, the presence of a circulating human Ca10 counterpart (Ca10H) in cancer patients and its correlation with tumor size and metastasis suggests important clinical implications in cancer treatment.
CELLULAR & MOLECULAR IMMUNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Ana Pozo-Rodriguez, Juan A. Mendez-Liter, Laura I. de Eugenio, Manuel Nieto-Dominguez, Eva Calvino, Francisco Javier Canada, Andres G. Santana, Jaime Diez, Juan L. Asensio, Jorge Barriuso, Alicia Prieto, Maria Jesus Martinez
Summary: The study explores the use of endoxylanases and their glycosynthase variants in the valorization of hemicellulosic residues and the synthesis of glycosides with improved properties. The results demonstrate the high catalytic efficiency and substrate versatility of these enzymes, particularly in the degradation of beechwood xylan and wheat arabinoxylan. The glycosynthase variant shows enhanced capacity in the synthesis of xylooligosaccharides and glycosylation of phenolic compounds with antioxidant properties.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)