Article
Chemistry, Multidisciplinary
Praneeth Bommisetti, Vahe Bandarian
Summary: This study provides critical insights into the biochemical mechanism underlying tRNA modification by the MnmEG. The formation of a flavin-iminium intermediate, FAD[N-5 & boxH;CH2](+), was identified as the central step in the MnmEG reaction, and it was demonstrated to be the universal intermediate for all MnmEG homologues. Additionally, a stable RNA-protein complex, possibly noncovalent in nature, was discovered.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Review
Biochemistry & Molecular Biology
Weifang Cui, Deze Zhao, Junjie Jiang, Faqing Tang, Chunfang Zhang, Chaojun Duan
Summary: tRNA is a highly conserved and abundant RNA species that plays a crucial role in protein translation. tRNA molecules undergo post-transcriptional modifications by tRNA modifying enzymes. With the rapid development of high-throughput sequencing technology, various types of tRNA modifications have been discovered in different research fields. In this review, we discuss the biological functions of tRNA modifications, including tRNA stability, protein translation, cell cycle regulation, oxidative stress response, and immunity. We also explore the implications of tRNA modifications in human diseases. Additionally, we review emerging techniques for the detection and characterization of tRNA modifications.
INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Gyuhyeok Cho, Jangmin Lee, Jungwook Kim
Summary: The uridine at the 34th position of tRNA can be modified to affect decoding properties during translation. MnmC enzyme in bacteria like Escherichia coli converts cmnm(5)(s(2))U to mnm(5)(s(2))U, while MnmM enzyme in Bacillus subtilis converts nm(5)(s(2))U to mnm(5)(s(2))U.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Martina Hager, Marie-Theres Poehler, Franziska Reinhardt, Karolin Wellner, Jessica Huebner, Heike Betat, Sonja Prohaska, Mario Moerl
Summary: CCA addition is a unique and highly accurate reaction in tRNA maturation. While the mechanism is well-known, it is still a mystery why bacterial and eukaryotic enzymes exhibit low tRNA substrate affinity but efficiently catalyze the reaction. Through the reconstruction and characterization of an ancestral enzyme from Gammaproteobacteria, researchers discovered that the ancestral enzyme has higher tRNA affinity and lower catalytic efficiency compared to the modern enzyme from Escherichia coli. They also found that the modern enzyme increased polymerization efficiency by reducing binding affinity to tRNA. This puzzling weak substrate interaction represents a distinct activity enhancement in the evolution of CCA-adding enzymes.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Review
Biochemistry & Molecular Biology
Amanda S. Byer, Xiaokun Pei, Michael G. Patterson, Nozomi Ando
Summary: Enzyme function requires conformational changes which are difficult to observe. However, small-angle X-ray scattering (SAXS) can provide rich insight into enzyme behavior, including subtle domain movements. Recent uses of SAXS to probe structural enzyme changes upon ligand and partner-protein binding are highlighted, along with tools for signal deconvolution of complex protein solutions.
CURRENT OPINION IN CHEMICAL BIOLOGY
(2023)
Article
Biochemical Research Methods
Lifeng Yang, Xiong Jiao
Summary: This study developed an alignment-free method for the classification of enzymes and non-enzymes, revealing that the topological and information-theoretic residue interaction network features perform better, and the combination of fast mode and slow mode can provide a better explanation for the classification results.
CURRENT BIOINFORMATICS
(2021)
Article
Endocrinology & Metabolism
Sabine Jung-Klawitter, Petra Richter, Yuheng Yuan, Karin Welzel, Marie Kube, Stella Baehr, Alexander Leibner, Egbert Flory, Thomas Opladen
Summary: This study analyzed 25 variants of tyrosine hydroxylase (TH) associated with dopa-responsive dystonia and investigated their influence on protein stability, activity, and cellular localization. The results identified different groups of variants based on their resistance to proteinase K digestion and cellular distribution. The study also found that some variants disrupt the physical interaction between TH and other proteins, affecting enzymatic activity.
JOURNAL OF INHERITED METABOLIC DISEASE
(2023)
Article
Biochemistry & Molecular Biology
John J. Kelly, Dale Tranter, Els Pardon, Gamma Chi, Holger Kramer, Lotta Happonen, Kelly M. Knee, Jay M. Janz, Jan Steyaert, Christine Bulawa, Ville O. Paavilainen, Juha T. Huiskonen, Wyatt W. Yue
Summary: The integrity of a cell's proteome relies on the correct folding of polypeptides, which is facilitated by the chaperonin TCP-1 ring complex (TRiC). Structural studies have provided insights into the architecture and substrate recognition of TRiC, but the fate of substrates inside the TRiC chamber has remained unclear. In this study, cryo-EM was used to determine the structure of endogenous human TRiC with substrates and cochaperone at different folding stages. The findings revealed the positioning of already-folded regions of client proteins at the chamber wall, allowing unstructured regions to achieve their native fold. The substrates engaged with different sections of the chamber during the folding process, while the cochaperone PhLP2A acted as a molecular strut between the substrate and TRiC chamber. These structural snapshots contribute to our understanding of client protein folding within TRiC.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Ranjan K. Singh, Ahmed Soliman, Giambattista Guaitoli, Eliza Stoermer, Felix von Zweydorf, Thomas Dal Maso, Asmaa Oun, Laura Van Rillaer, Sven H. Schmidt, Deep Chatterjee, Joshua A. David, Els Pardon, Thomas U. Schwartz, Stefan Knapp, Eileen J. Kennedy, Jan Steyaert, Friedrich W. Herberg, Arjan Kortholt, Christian Johannes Gloeckner, Wim Versees
Summary: Mutations in the LRRK2 gene are a leading cause of Parkinson's disease, while overactivation of LRRK2 is associated with idiopathic form of the disease. Researchers have identified and characterized nanobodies that can bind to different domains of LRRK2 and inhibit or activate its activity. These nanobodies act through an allosteric inhibitor mechanism and provide potential therapeutic strategies for Parkinson's disease.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
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