Article
Biochemistry & Molecular Biology
Marzuq A. Ungogo, Mustafa M. Aldfer, Manal J. Natto, Hainan Zhuang, Robyn Chisholm, Katy Walsh, MarieClaire McGee, Kayhan Ilbeigi, Jamal Ibrahim Asseri, Richard J. S. Burchmore, Guy Caljon, Serge Van Calenbergh, Harry P. De Koning
Summary: African Animal Trypanosomiasis (AAT) is a fatal livestock disease in Sub-Saharan Africa caused by Trypanosoma brucei brucei, T. vivax, and T. congolense. Limited treatment options and resistance threaten the control of this disease. In this study, the adenosine transporters of T. vivax (TvxNT3) and T. congolense (TcoAT1/NT10) were characterized and their functional expression was demonstrated. The findings suggest that nucleoside chemotherapy for AAT is viable based on the similarities in nucleoside sensitivity among different parasite species and the interactions with nucleoside transporters.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Stefanie Neun, Paul Brear, Eleanor Campbell, Theodora Tryfona, Kamel El Omari, Armin Wagner, Paul Dupree, Marko Hyvonen, Florian Hollfelder
Summary: The abundance of protein sequence data is not matched by the number of experimentally verified functional annotations. In this study, we used high-throughput microfluidic droplet screening to identify a new beta-glucuronidase enzyme with little homology to previously studied enzymes. This finding demonstrates the potential of functional metagenomics in uncovering the function of enzymes that cannot be predicted by bioinformatics.
NATURE CHEMICAL BIOLOGY
(2022)
Article
Chemistry, Physical
Guoqing Zhai, Rong Gong, Yaxin Lin, Meng Zhang, Jiahui Li, Zixin Deng, Jiazhong Sun, Wenqing Chen, Zhengyu Zhang
Summary: This study reports the crystal structures of the non-heme Fe2+/2OG-dependent halogenase AdaV and reveals its catalytic mechanism. The study also demonstrates the engineering of AdaV variants to produce different halogenated and hydroxylated products, and proposes a dual-controlling mechanism for AdaV catalysis.
Article
Energy & Fuels
Haoyun Liu, Zhen Zhang, Qi Yuan, Yaming Zhou, Jing Liu, Hongmin Yang
Summary: Single-atom catalysts (SACs) have high potential in heterogeneous catalytic processes due to their high atomic utilization efficiency and controllable active sites. This study focuses on the design and investigation of single transition metal atom doped h-BN vacancy catalysts for the cost-effective Hg-0 oxidation by O-2. The results show that Fe/V-B-BN catalyst exhibits excellent affinity to Hg-0 and follows the Eley-Rideal mechanism for the oxidation process. The outcomes demonstrate that Fe/V-B-BN catalyst is a promising candidate for cleaner coalfired power plant operations.
Article
Chemistry, Physical
Juanjuan Zhao, Xiaoxiong Wang, Peng Dai
Summary: The photocatalytic performances of two Cu(II) complexes were studied by photodegrading MB dye under UV light, demonstrating good degradation ability and potential degradation mechanism. The LC-MS was used to analyze the catalytic process, while recycling experiments proved the photocatalyst's reusability and stability.
JOURNAL OF MOLECULAR STRUCTURE
(2021)
Article
Thermodynamics
Kaikai Kou, Wei Zhou, Shuai Chen, Jihui Gao
Summary: The oxidation mechanism of carboxyl group in coal was systematically investigated by preparing a model compound of carboxylated graphene, providing essential guidance for the application of CAWE. Energies for hydrogen production and Fe2+ generation were significantly reduced in the process, demonstrating the potential for reducing electric energy consumption in H-2 production.
Article
Engineering, Environmental
Xinfu Zhao, Xibin Yi, Jianjun Song, Xiaoying Yuan, Shimo Yu, Yihao Nie, Jing Zhang, GeGe Cao
Summary: In this study, a mesoporous and flexible polyimide (PI) aerogel membrane was selected as a peroxymonosulfate (PMS) activator, demonstrating efficient degradation of organic contaminants. The degradation rate of the PI/PMS aerogel system without adsorption-desorption equilibrium stage was found to be 2.5 times faster than the catalyst with adsorption-desorption equilibrium stage. Furthermore, the PI/PMS membrane system showed consistent high performance in removing AO7 even after multiple cycles.
CHEMICAL ENGINEERING JOURNAL
(2022)
Article
Materials Science, Composites
Zefu Li, Shuo Wang, Wenxuan Ding, Yonglin Chen, Meng Chen, Shujie Zhang, Zhuangjian Liu, Weidong Yang, Yan Li
Summary: This study presents a flexible porous bimodal pressure sensor by fabricating 3D microstructured sensitive porous carbon-nanotubes composites. The sensor can switch between piezoresistive and piezocapacitive sensing modes without altering the device structure, and offers high sensitivity, wide measuring range, rapid response time, and long-term durability. A mechanical constitutive model is proposed to explain the sensing mechanism of the sensor. Multiple sensors are used to monitor 3D printing manufacturing stress, structure assembling stress, and human physiology signals in real-time.
COMPOSITES SCIENCE AND TECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Kaiyue Qian, Wenyi Yang, Xiaolei Chen, Yongzhong Wang, Min Zhang, Mingzhu Wang
Summary: This study reported the crystal structure of a protein called Amuc_2109 from Akkermansia muciniphila, which is associated with intestinal health. Biochemical assays showed that Amuc_2109 is a GlcNAc-specific glycosidase with a wide range of enzymatic activity, indicating its survival advantage in the intestinal environment. These findings contribute to the understanding of the catalytic mechanism of Amuc_2109 and the molecular mechanism of complex carbohydrate utilization and restoration of the intestinal barrier in A. muciniphila.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Materials Science, Multidisciplinary
Jian-Qiu Huang, Woon Gie Chong, Biao Zhang, Xinyue Ma
Summary: In the past two decades, significant attention has been paid to developing novel electrodes to enhance battery performance. The introduction of multi-functional freestanding films called interlayers between anodes and cathodes has proven to be crucial in improving the electrochemical performance of batteries. These interlayers play essential roles in various rechargeable battery systems, offering opportunities for advanced battery development through structural design, component optimization, and function mechanism assessment.
MATERIALS TODAY COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Moez Rhimi, Jean-Luc Da Lage, Richard Haser, Georges Feller, Nushin Aghajari
Summary: Insects rely on carbohydrates like starch and glycogen for energy, and α-amylases play essential roles under extreme conditions, contributing to their survival. Drosophila melanogaster α-amylase, DMA, is active over a broad temperature and pH range, and its crystal structures reveal an adaptive response to temperature variations.
Article
Biochemistry & Molecular Biology
Taein Park, Huyen Nga Hoang, Jung Youn Kang, Jongseo Park, Sang A. Mun, Minwoo Jin, Jihyeong Yang, Che-Hun Jung, Soo Hyun Eom
Summary: During glycerol metabolism, glycerol dehydrogenase (GDH) catalyzes the initial step of glycerol oxidation using a NAD(+)-dependent kinetic mechanism. Crystal structures of GDH with a substrate analogue bound in the presence or absence of NAD(+) were determined, revealing a flexible beta-hairpin that undergoes reduced flexibility upon NAD(+) binding. This alterable flexibility of the beta-hairpin contributes to cofactor binding and the catalytic efficiency of GDH.
Article
Biochemistry & Molecular Biology
Giovanni Bisello, Katarzyna Kusmierska, Marcel M. Verbeek, Jolanta Sykut-Cegielska, Michel A. A. P. Willemsen, Ron A. Wevers, Krystyna Szymanska, Jaroslaw Poznanski, Jakub Drozak, Katarzyna Wertheim-Tysarowska, Agnieszka Magdalena Rygiel, Mariarita Bertoldi
Summary: Aromatic amino acid decarboxylase (AADC) deficiency is a rare monogenic disease that causes intellectual disability, movement disorders, and autonomic dysfunction. In this study, a novel mutation of AADC was identified, which resulted in a significant decrease in enzymatic activity. The defect was found to be due to the mispositioning of the catalytically competent intermediate. These findings provide insights into the pathogenesis of AADC deficiency and a potential target for precision therapy.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Article
Thermodynamics
Xiaoxue Cheng, Ding Jiang, Bin Cao, Shuang Wang, Hongping Li, Bahram Barati, Zhen Xia, Jinsong Zhou, Shurong Wang
Summary: In this study, the products and reaction mechanisms of cellulose during non-catalytic and catalytic pyrolysis with ZSM-5 catalyst were analyzed using Py-GC/MS and DFT. The results showed that catalytic pyrolysis reduced the furan content and introduced aromatic hydrocarbons as new components. DFT studies demonstrated the involvement of hydrogen proton at the catalyst's acid sites in most cellulose pyrolysis reactions. Catalytic pyrolysis significantly lowered the activation energy for dehydration and de-carbonylation compared to non-catalytic pyrolysis.
COMBUSTION AND FLAME
(2022)
Article
Biophysics
Zachariah M. Ingram, David A. Schneider, Aaron L. Lucius
Summary: RNA polymerase I shows significant variability in nucleotide incorporation rate constants, with faster values observed for the first two nucleotide incorporations compared to the remaining seven positions. Additionally, the enzyme exhibits a higher affinity for GTP compared to ATP. Understanding the differences between Pol enzymes will provide insight into the evolutionary pressures that led to their specialized roles.
BIOPHYSICAL JOURNAL
(2021)
Article
Neurosciences
Eleftherios Zarkadas, Eva Pebay-Peyroula, Mackenzie John Thompson, Guy Schoehn, Tomasz Uchanski, Jan Steyaert, Christophe Chipot, Francois Dehez, John Edward Baenziger, Hugues Nury
Summary: This study used cryo-EM to determine the structure of the muscle-type nicotinic acetylcholine receptor from the electric fish Torpedo. The results shed light on the structural changes and functional states of the receptor, uncovering the important role of subunits in channel gating and explaining the lower potency of nicotine at muscle nicotinic receptors compared to neuronal ones.
Article
Multidisciplinary Sciences
Jeremy R. Keown, Zihan Zhu, Loic Carrique, Haitian Fan, Alexander P. Walker, Itziar Serna Martin, Els Pardon, Jan Steyaert, Ervin Fodor, Jonathan M. Grimes
Summary: Influenza A viruses cause significant burdens to healthcare systems through seasonal epidemics and global pandemics. The viral RNA-dependent RNA polymerase plays a central role in the replication cycle of influenza viruses and is a potential target for antiviral development. By characterizing the inhibitory effect of nanobodies on the 1918 pandemic influenza virus polymerase complex, sensitive sites interfering with polymerase activity in vitro were identified, suggesting them as effective targets for potential influenza antiviral development.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Maxime Killer, Giada Finocchio, Haydyn D. T. Mertens, Dmitri I. Svergun, Els Pardon, Jan Steyaert, Christian Loew
Summary: Proton-coupled Oligopeptide Transporters (POTs) mediate the uptake of short di- and tripeptides. This study determined the structure of DtpC and provided insights into its ligand specificity using cryogenic electron microscopy (cryo-EM). The research highlights the value of nanobodies for structure determination of low molecular weight integral membrane proteins.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Lorenzo Maso, Filippo Vascon, Monica Chinellato, Frederic Goormaghtigh, Pierangelo Bellio, Enrica Campagnaro, Laurence Van Melderen, Maria Ruzzene, Els Pardon, Alessandro Angelini, Giuseppe Celenza, Jan Steyaert, Donatella Tondi, Laura Cendron
Summary: Antimicrobial resistance poses a threat to eradicating infectious diseases and reducing the effectiveness of available treatments. The bacterial SOS pathway is a key mechanism leading to resistance, and inhibiting this pathway may delay the evolution of antimicrobial resistance. In this study, nanobodies that bind to and block the SOS response in Escherichia coli were identified, paving the way for the development of new-generation antibiotic adjuvants for treating bacterial infections.
Article
Multidisciplinary Sciences
Liselot Dewachter, Aaron N. N. Brooks, Katherine Noon, Charlotte Cialek, Alia Clark-ElSayed, Thomas Schalck, Nandini Krishnamurthy, Wim Versees, Wim Vranken, Jan Michiels
Summary: Deep mutational scanning is a powerful method for investigating protein function and stability. In this study, the researchers perform deep mutational scanning on three essential E. coli proteins and study the effects of mutations in their original genomic context. They use over 17,000 protein variants to explore protein function and the importance of individual amino acids. The study also evaluates resistance development against antimicrobial compounds and identifies potential targets for drug development.
NATURE COMMUNICATIONS
(2023)
Correction
Multidisciplinary Sciences
Liselot Dewachter, Aaron N. Brooks, Katherine Noon, Charlotte Cialek, Alia Clark-ElSayed, Thomas Schalck, Nandini Krishnamurthy, Wim Versees, Wim Vranken, Jan Michiels
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Kevin Van Holsbeeck, Baptiste Fischer, Simon Gonzalez, Charlene Gadais, Wim Versees, Jose C. Martins, Charlotte Martin, Alexandre Wohlkoenig, Jan Steyaert, Steven Ballet
Summary: RAS proteins play a crucial role in regulating intracellular signaling networks and mutations that stabilize their active state are associated with cancer development. The study investigated the potential of developing peptide mimetics to modulate RAS signaling by mimicking the complementarity-determining region 3 (CDR3) of the regulatory guanine nucleotide exchange factor (GEF) son of sevenless 1 (SOS1). Through optimization and conformational rigidification, CDR3 mimetics with half of the maximal activation potential of Nanobody14 (Nb14) were obtained, demonstrating the feasibility of modulating protein-protein interactions through structural mimicry of a paratope.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Neurosciences
Adekunle T. Bademosi, Marianna Decet, Sabine Kuenen, Carles Calatayud, Jef Swerts, Sandra F. Gallego, Nils Schoovaerts, Spyridoula Karamanou, Nikolaos Louros, Ella Martin, Jean-Baptiste Sibarita, Katlijn Vints, Natalia V. Gounko, Frederic A. Meunier, Anastassios Economou, Wim Versees, Frederic Rousseau, Joost Schymkowitz, Sandra-F. Soukup, Patrik Verstreken
Summary: Neuronal activity-induced calcium influx is connected to synaptic autophagy and neuronal survival through Endophilin-A in a Parkinson disease-relevant fashion. Mutations in the disordered loop of Endophilin-A render it insensitive to neuronal stimulation, affecting protein dynamics and autophagosome formation. Balanced stimulation-induced autophagy is critical for dopaminergic neuron survival, and a variant in the human ENDOA1 disordered loop conferring risk to Parkinson disease also blocks nanodomain protein mobility and autophagy in vivo and in human-induced dopaminergic neurons.
Article
Biochemistry & Molecular Biology
Babette Deckers, Silke Vercauteren, Veerke De Kock, Charlotte Martin, Tamas Lazar, Pauline Herpels, Liselot Dewachter, Natalie Verstraeten, Eveline Peeters, Steven Ballet, Jan Michiels, Christian Galicia, Wim Versees
Summary: This study identifies the DNA-binding protein YbiB as an interactor of the bacterial protein ObgE. The study also reveals the binding site between the C-terminal domain of ObgE and the positively charged groove on the surface of YbiB. Additionally, ObgE competes with DNA for binding to YbiB, indicating its role in the cellular processes involving YbiB.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Scott A. Jones, Prerana Gogoi, Jonathan J. Ruprecht, Martin S. King, Yang Lee, Thomas Zogg, Els Pardon, Deepak Chand, Stefan Steimle, Danielle M. Copeman, Camila A. Cotrim, Jan Steyaert, Paul G. Crichton, Vera Moiseenkova-Bell, Edmund R. S. Kunji
Summary: Mitochondrial uncoupling protein 1 (UCP1) is responsible for the ability of brown adipose tissue in mammals to burn calories as heat for thermoregulation. UCP1 can be activated by fatty acids to generate heat by catalyzing the leakage of protons across the mitochondrial inner membrane. However, purine nucleotides can bind and inhibit UCP1, regulating proton leak through an unknown molecular mechanism. The cryo-electron microscopy structure of the GTP-inhibited state of UCP1 provides insights into the specific interactions and pH dependency of the regulatory mechanism, indicating that inhibitor binding prevents the conformational changes necessary for proton leak.
Article
Biochemical Research Methods
A. Breine, K. Van Holsbeeck, C. Martin, S. Gonzalez, M. Mannes, E. Pardon, J. Steyaert, H. Remaut, S. Ballet, C. van der Henst
Summary: Membrane interactions greatly influence the mode of action of proteins, cell-penetrating peptides, and antimicrobial peptides. A recent study discovered a nanobody that interacts with the multidrug-resistant bacteria Acinetobacter baumannii, but it only binds to fixed cells. To overcome this limitation, linear peptides corresponding to the complementarity-determining regions (CDR) were synthesized and labeled with fluorescent tags. Microscopy data showed that the CDR3 sequence has clear membrane interactions with living A. baumannii cells, indicating its importance in binding and avoiding cell permeabilization. The cyclization of the peptide with a rigidifying 1,2,3-triazole bridge retained its binding ability and provided proteolytic protection. Overall, this study led to the discovery of novel peptides that bind a multidrug-resistant pathogen.
BIOCONJUGATE CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Arum Wu, David Salom, John D. Hong, Aleksander Tworak, Kohei Watanabe, Els Pardon, Jan Steyaert, Hideki Kandori, Kota Katayama, Philip D. Kiser, Krzysztof Palczewski
Summary: By discovering specific Nbs that bind to the extracellular surface of rhodopsin and modulate the thermodynamics of its activation process, researchers have revealed the secondary structure of Nbs and how they affect GPCR signaling states. Nbs also improve protein misfolding in disease-associated mutant rhodopsin, making them potential therapeutic agents for related diseases.
NATURE COMMUNICATIONS
(2023)
Meeting Abstract
Biochemistry & Molecular Biology
F. Vascon, L. Maso, M. Chinellato, Y. Bouchiba, E. Campagnaro, S. De Felice, F. Goormaghtigh, P. Bellio, G. Cioci, A. Angelini, G. Celenza, S. Barbe, L. Van Melderen, J. Steyaert, E. Pardon, D. Tondi, L. Cendron
Meeting Abstract
Biophysics
John E. Baenziger, Eleftherios Zarkadas, Eva Pebay-Peyroula, Mackenzie Thompson, Guy Schoehn, Tomasz Uchanski, Jan Steyaert, Christophe J. Chipot, Francois Dehez, Hugues Nury
BIOPHYSICAL JOURNAL
(2022)
