Article
Chemistry, Organic
Brian J. J. Timmer, Tiddo J. Mooibroek
Summary: The article introduces a simple dipyridyl ligand that can form ring-like complexes with Pd2+ ion, and its metal complexes show potential biological applications in selectively binding glycosides.
EUROPEAN JOURNAL OF ORGANIC CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Brian J. J. Timmer, Arjaan Kooijman, Xander Schaapkens, Tiddo J. Mooibroek
Summary: Galectins are a subclass of carbohydrate binding proteins that play a role in various biological processes. A synthetic galectin mimic with high selectivity for a specific galactoside has been designed and synthesized for the first time, showing a selectivity over 65-fold compared to a glucoside.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Multidisciplinary
Jon I. Quintana, Sandra Delgado, Reyes Nunez-Franco, F. Javier Canada, Gonzalo Jimenez-Oses, Jesus Jimenez-Barbero, Ana Arda
Summary: Gal-4 consists of two different domains that preferentially bind to A and B histo blood group antigens with different affinities. The study used NMR, ITC, and molecular modeling to investigate the binding of the N-terminal domain of Gal-4 to a group of differently presented A and B oligosaccharide antigens in solution, providing a structural-based rationale for the observed binding preferences.
FRONTIERS IN CHEMISTRY
(2021)
Review
Chemistry, Analytical
Mengnan Li, Haijie Ji, Yuhan Wang, Chi Zhang, Xian Zhang, Yiqi Wu, Feiyun Cui, Qin Zhou
Summary: Glycans and lectins have shown promise as alternative receptors in the development of biosensors for viral detection. This article provides insights into the interactions between glycans and lectins, viruses, and host cells. It summarizes the strategies for developing glycan and lectin biosensors and discusses their applications in various viruses. The challenges and future trends in the advancement of glycan-related biosensors are also emphasized.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Review
Biochemistry & Molecular Biology
Gradimir Misevic, Emanuela Garbarino
Summary: The binding of glycans to glycans plays a significant role in xenogeneic self-recognition and adhesion in sponges, cell compaction in mouse embryos, and in vitro tumor cell adhesion in mammals. This intermolecular recognition process is considered a new paradigm in cellular interactions. Glycan structures in sponges have unique species-specific sequences, and their binding mechanism relies on specific interactions of small oligosaccharide motifs.
Review
Biochemistry & Molecular Biology
Laura L. Kiessling, Roger C. Diehl
Summary: The text discusses how proteins recognize sugars through CH-π interactions, highlighting the importance of electron-rich aromatic residues in glycan binding.
ACS CHEMICAL BIOLOGY
(2021)
Article
Microbiology
Theodore J. Kottom, Eva M. Carmona, Kyle Schaefbauer, Andrew H. Limper
Summary: In this study, two new C-type lectin receptors (CLRs) that recognize Pneumocystis cell wall components were investigated. The results showed significant binding between these CLRs and Pneumocystis, and increased expression of these receptors during infection. Further studies using CLR deficient mice will provide more insights into the host immune response to Pneumocystis.
JOURNAL OF MEDICAL MICROBIOLOGY
(2023)
Review
Biotechnology & Applied Microbiology
Jane Wittrup Agger, Michael Schmidt Madsen, Line Korte Martinsen, Pedro Alves Martins, Kristian Barrett, Anne S. Meyer
Summary: This review summarizes the latest research on glucuronoyl esterases (GEs), with a focus on fungal variants. The study reveals that fungal enzymes largely fall into one major branch, with only a minor subset of bacterial enzymes in the same branch. Additionally, some fungal proteins carry a CBM1 binding domain. Molecular docking experiments suggest that there are no direct interactions between the enzyme and lignin polymer, and an elongated carbon chain between the ester linkage and the first phenyl of lignin is preferred. The next step for these enzymes is to explore their application in utilizing lignocellulose as a renewable resource.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Fisheries
Areli Silva-Becerril, Adrian Quintero-Martinez, Alejandra Hernandez-Santoyo
Summary: A galacturonic acid-specific lectin, AcL, was purified from the sea hare Aplysia californica using galactose-agarose affinity chromatography. AcL has a molecular mass of 27.5 kDa and shows high affinity for D-galacturonic acid and low affinity for galactosides.
FISH & SHELLFISH IMMUNOLOGY
(2023)
Article
Materials Science, Biomaterials
Takahiro Oh, Takeshi Uemura, Masanori Nagao, Yu Hoshino, Yoshiko Miura
Summary: The study reveals that the interaction between glycopolymers carrying monosaccharides of mannose is much stronger than that between other saccharides. This finding is significant for understanding the interactions of carbohydrates on cell surfaces.
JOURNAL OF MATERIALS CHEMISTRY B
(2022)
Article
Chemistry, Physical
Morgan L. Nance, Jason W. Labonte, Jared Adolf-Bryfogle, Jeffrey J. Gray
Summary: Carbohydrate chains play a crucial role in regulating biological functions through interactions with protein receptors. The GlycanDock algorithm developed for protein-glycoligand docking refinement shows potential in high-resolution structural studies and can address experimental challenges. This algorithm has the ability to sample and discriminate among protein-glycoligand models with statistical reliability, making it a valuable tool in glycosciences research acceleration.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Biochemistry & Molecular Biology
Ekaterina D. Kazakova, Dmitry V. Yashunsky, Nikolay E. Nifantiev
Summary: The synthesis of the spacered A trisaccharide was achieved by employing a glycosyl donor with stereocontrolling groups, resulting in efficient and stereoselective formation of the required alpha-glycosylation product. The final products were deprotected and subjected to spacer biotinylation for use in biochemical studies.
Review
Multidisciplinary Sciences
Yu Nakagawa, Yukishige To
Summary: This article introduces the significance of Pradimicins (PRMs) and their application in glycobiological research. It proposes a new approach to address the aggregation issue of PRMs and presents recent attempts to develop PRM-based research tools.
PROCEEDINGS OF THE JAPAN ACADEMY SERIES B-PHYSICAL AND BIOLOGICAL SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Alexandra Tsouka, Kassandra Hoetzel, Marco Mende, Jasmin Heidepriem, Grigori Paris, Stephan Eickelmann, Peter H. Seeberger, Bernd Lepenies, Felix F. Loeffler
Summary: Multivalent ligand-protein interactions play a crucial role in enhancing the affinity and specificity of weak single glycan-protein interactions. Laser-based technology allows for in situ chemical synthesis of peptide scaffolds on functionalized glass slides, resulting in spatially defined multivalent glycopeptides. The study showed that surface functionalization, wettability, accessibility, and flexibility are essential factors in these interactions, and different types of surface functionalization and spacers may be required for optimal binding between lectins and glycans.
FRONTIERS IN CHEMISTRY
(2021)
Article
Chemistry, Medicinal
Alan Fernando Rodriguez Serrano, I-Ming Hsing
Summary: Understanding the interactions between aptamers and ligands is important for designing aptamer-based systems. This study used independent simulations and multiple metastable conformations to accurately predict binding sites, providing valuable insights for aptamer design and applications.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Infectious Diseases
Sue C. Nang, Mengyao Li, Marina Harper, Eric Mandela, Phillip J. Bergen, Jean-Marc Rolain, Yan Zhu, Tony Velkov, Jian Li
Summary: This study investigated the concentration-dependent transcriptomic responses of mcr-harbouring E. coli to polymyxin treatment. The results revealed that cell envelope remodelling, pEtN modification, iron acquisition, and oxidative stress protective mechanisms play a key role in the survival of mcr-carrying E. coli treated with polymyxin.
INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS
(2022)
Article
Food Science & Technology
Chongshan Dai, Subhajit Das Gupta, Zhanhui Wang, Haiyang Jiang, Tony Velkov, Jianzhong Shen
Summary: In this review, the authors summarized the current knowledge and challenges related to T-2 toxin-induced cardiotoxicity, and discussed potential treatment approaches. The cardiotoxicity caused by T-2 toxin involves various cellular pathways and mechanisms, including oxidative stress, mitochondrial dysfunction, and inflammatory responses. Antioxidant supplementation, induction of autophagy, and blockade of inflammatory signaling may provide protective effects against T-2 toxin-induced cardiac toxicity.
FOOD AND CHEMICAL TOXICOLOGY
(2022)
Article
Multidisciplinary Sciences
Rajnikant Sharma, Shekhar Yeshwante, Quentin Valle, Maytham Hussein, Varsha Thombare, Sean Michael McCann, Robert Maile, Jian Li, Tony Velkov, Gauri Rao
Summary: This article presents a simple and reproducible rat burn model that mimics clinical situations and induces immune dysregulation and bacterial infections. This model is of considerable utility for the development of new topical antibiotic drugs for burn wound and infections.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2022)
Article
Biotechnology & Applied Microbiology
Janice W. -Y. Mui, David P. De Souza, Eleanor C. Saunders, Malcolm J. McConville, Spencer J. Williams
Summary: The microbial degradation of sulfoquinovose through sulfoglycolysis allows the utilization of its carbon content and contributes to the biomineralization of its sulfur.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Microbiology
Arashdeep Kaur, Nichollas E. Scott, Marion Herisse, Ethan D. Goddard-Borger, Sacha Pidot, Spencer J. Williams
Summary: This study discovered two Paenarthrobacter spp. (Paenarthrobacter nitrojuajacolis LG01 and Paenarthrobacter histidinolovorans LG02) that can degrade levoglucosan as the sole carbon source. By genome sequencing and proteomics analysis, the researchers found the expression of a series of genes encoding known levoglucosan degrading enzymes, which are generally conserved in various bacteria. The findings reveal the diversity of how bacteria utilize levoglucosan as a nutrient source.
ARCHIVES OF MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Ilona Turek, Trang H. Nguyen, Charles Galea, Isaiah Abad, Lubna Freihat, David T. Manallack, Tony Velkov, Helen Irving
Summary: Interleukin-1 receptor-associated kinase 3 (IRAK3) regulates cellular responses to IL-1Rs and TLRs, leading to decreased pro-inflammatory cytokines and suppressed inflammation. The mechanism of IRAK3's action is unknown, but it functions as a guanylate cyclase and its cGMP product inhibits NF-κB activity. By mutagenesis and analysis, we identified residues in and near the catalytic center of IRAK3 that affect NF-κB activity and subcellular localization in HEK293T cells. Mutant IRAK3 variants with reduced cGMP generation capacity and altered NF-κB activity fail to rescue IRAK3 function in LPS-stimulated THP-1 monocytes unless a cGMP analog is present.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Medicinal
Nitin A. Patil, Wendong Ma, Xukai Jiang, Xiaoji He, Heidi H. Yu, Hasini Wickremasinghe, Jiping Wang, Philip E. Thompson, Tony Velkov, Kade D. Roberts, Jian Li
Summary: Polymyxins, including polymyxin B and colistin, are used as a last resort to treat life-threatening multidrug-resistant Gram-negative bacterial infections. However, their clinical use is limited by toxicity and increasing resistance. This study explores the role of the conserved position 10 threonine residue in polymyxin's structure and reveals the requirements for antibacterial activity. These findings provide vital information for developing safer and more effective next-generation polymyxin antibiotics.
JOURNAL OF MEDICINAL CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Iris D. D. Zelnik, Beatriz Mestre, Jonathan J. J. Weinstein, Tamir Dingjan, Stav Izrailov, Shifra Ben-Dor, Sarel J. J. Fleishman, Anthony H. H. Futerman
Summary: Researchers validate a one-step algorithm called mPROSS for stabilizing membrane proteins directly from an AlphaFold2 model structure. By applying this algorithm to ceramide synthase, they obtained a more stable form of human CerS2 enzyme through 37 designed mutations. With the help of molecular dynamics simulations, a potential pathway for substrate delivery to ceramide synthases is proposed.
NATURE COMMUNICATIONS
(2023)
Article
Infectious Diseases
Mengyao Li, Mohammad A. K. Azad, Philip E. Thompson, Kade D. Roberts, Tony Velkov, Yan Zhu, Jian Li
Summary: Polymyxins are last-line antibiotics used to treat Gram-negative 'superbugs'. However, they can cause nephrotoxicity in up to 60% of patients. This study investigated the transcriptomic responses of human renal tubular cells to polymyxins and identified potential targets for designing safer new-generation polymyxins.
Article
Biochemistry & Molecular Biology
Marion Herisse, Keishi Ishida, Jordan Staiger-Creed, Louise Judd, Spencer J. Williams, Benjamin P. Howden, Timothy P. Stinear, Hans-Martin Dahse, Kerstin Voigt, Christian Hertweck, Sacha J. Pidot
Summary: Nocardia are opportunistic human pathogens that cause difficult to treat infections. However, little is known about their involvement in the pathogenesis and the natural products they produce. In this study, a new cytotoxic and antifungal polyene called terpenomycin was discovered in a human pathogenic Nocardia terpenica isolate. The biosynthetic pathway and unique features of terpenomycin were revealed, and a mutant library helped identify a terpenomycin-null mutant. These findings highlight the potential of neglected actinomycetes as producers of diverse bioactive molecules.
ACS CHEMICAL BIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Betty Exintaris, Nilushi Karunaratne, Elizabeth Yuriev
Summary: Successful problem solving requires a range of cognitive skills and awareness, including content knowledge, critical thinking, metacognition, and conceptual reasoning. Teaching strategies that support problem-solving skills involve providing examples, scaffolding metacognition, and allowing for critical evaluation. This study explores a classroom activity that combines metacognitive scaffolding, problem-solving practice, and evaluating AI-generated solutions. The findings suggest that students benefit from metacognition in problem solving and show an understanding of the collaborative nature of this process. Additionally, incoming university students may need support to develop advanced critical-thinking skills.
JOURNAL OF CHEMICAL EDUCATION
(2023)
Editorial Material
Chemistry, Multidisciplinary
Elizabeth Yuriev, Donald J. Wink, Thomas A. Holme
Summary: The Journal of Chemical Education is calling for papers on the emerging applications of generative artificial intelligence (AI). The virtual special issue aims to collect reports and establish baselines of understanding for tools such as ChatGPT.
JOURNAL OF CHEMICAL EDUCATION
(2023)
Article
Chemistry, Multidisciplinary
Garth Cameron, Tram Nguyen, Marcin Ciula, Spencer J. Williams, Dale I. Godfrey
Summary: Natural Killer T (NKT) cells are a type of T cell subset that recognize lipid antigens and have diverse functional properties. The commensal organism Bacteroides fragilis produces various forms of alpha-galactosylceramide (alpha GC), a lipid antigen target for NKT cells. The total synthesis of a major form of alpha GC from B. fragilis (Bf alpha GC) and several analogues was reported, and their recognition by mouse and human NKT cells was confirmed. NKT cells experienced with Bf alpha GC displayed regulatory function and inhibited the expansion of naive NKT cells and antigen-stimulated mucosal-associated invariant T (MAIT) cells, revealing the broad immunoregulatory activity of B. fragilis-derived NKT cell agonists.
Article
Crystallography
Phillip L. van der Peet, Rohan D. Joyce, Holger Ott, Sebastian M. Marcuccio, Jonathan M. White, Spencer J. Williams
Summary: The crystal structure of the title compound reveals strong hydrogen bonds and interactions, forming infinite chains along the c-axis direction.
ACTA CRYSTALLOGRAPHICA SECTION E-CRYSTALLOGRAPHIC COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Maytham Hussein, Labell J. M. Wong, Jinxin Zhao, Vanessa E. Rees, Rafah Allobawi, Rajnikant Sharma, Gauri G. Rao, Mark Baker, Jian Li, Tony Velkov
Summary: This study investigates the synergistic antibacterial activity of polymyxin B in combination with the antifungal caspofungin against Klebsiella pneumoniae, and analyzes the killing mechanisms of this combination.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)