Article
Biochemistry & Molecular Biology
Gaetano D'Urso, Sophie Chat, Reynald Gillet, Emmanuel Giudice
Summary: This study provides a high-resolution description of the multidomain ribosomal protein bS1, revealing new conformations of OB1 and OB2 and highlighting their roles in mRNA binding and accommodation on the ribosome.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Emily J. Rundlet, Mikael Holm, Magdalena Schacherl, S. Kundhavai Natchiar, Roger B. Altman, Christian M. T. Spahn, Alexander G. Myasnikov, Scott C. Blanchard
Summary: Research has shown that the bacterial GTPase elongation factor G specifically engages ribosome conformations achieved spontaneously in an active, GTP-bound state to facilitate translocation reactions. These findings suggest that processes intrinsic to the ribosome complex may regulate protein synthesis rates, with energy expenditure occurring later in the translocation mechanism than previously proposed.
Article
Multidisciplinary Sciences
Valentyn Petrychenko, Bee-Zen Peng, Ana C. de A. P. Schwarzer, Frank Peske, Marina V. Rodnina, Niels Fischer
Summary: In this study, the researchers visualized the mechanism of EF-G in the ribosome translocation process using time-resolved cryo-EM, revealing the crucial role of GTP hydrolysis in promoting the movement of the ribosome along mRNA.
NATURE COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Kristopher W. Brannan, Isaac A. Chaim, Ryan J. Marina, Brian A. Yee, Eric R. Kofman, Daniel A. Lorenz, Pratibha Jagannatha, Kevin D. Dong, Assael A. Madrigal, Jason G. Underwood, Gene W. Yeo
Summary: The STAMP technique efficiently detects RBP-RNA interactions and reveals the dynamic regulation of RBPs in single cells. Pairing with long-read sequencing allows for isoform-specific RBP target site identification, while Ribo-STAMP can measure transcriptome-wide ribosome association in cells.
Article
Biochemistry & Molecular Biology
Chris Papadopoulos, Isabelle Callebaut, Jean-Christophe Gelly, Isabelle Hatin, Olivier Namy, Maxime Renard, Olivier Lespinet, Anne Lopes
Summary: The noncoding genome is crucial for the birth of novel genes and genetic novelty. By characterizing amino acid sequences encoded by intergenic ORFs of S. cerevisiae, it was found that they contain elementary building blocks of protein structures and exhibit a large structural diversity similar to canonical proteins. The study also highlighted the early stages of de novo gene birth and revealed a strong correlation between the fold potential of de novo proteins and ancestral amino acid sequences, indicating the relationship between the noncoding genome and protein structure.
Article
Multidisciplinary Sciences
Hu Zeng, Jiahao Huang, Jingyi Ren, Connie Kangni Wang, Zefang Tang, Haowen Zhou, Yiming Zhou, Hailing Shi, Abhishek Aditham, Xin Sui, Hongyu Chen, Jennifer A. Lo, Xiao Wang
Summary: The precise control of mRNA translation is crucial in posttranscriptional gene regulation, but it is challenging to study it systematically at the transcriptomic scale with spatial and single-cell resolution. The researchers developed a method called RIBOmap to detect cellular translatome. The study revealed cell cycle-dependent translational control and colocalized translation of functional gene modules.
Article
Biochemistry & Molecular Biology
Xiang Meng, Alan Reed, Sandie Lai, Juraj Szavits-Nossan, John E. G. McCarthy
Summary: Gene expression stochasticity is an inherent feature of biological systems, creating non-genetic cellular variation and influencing various processes. In this study, the researchers discovered a distinct form of non-transcriptional noise associated with the translation machinery and mRNA 5'UTR of the GCN4 gene in yeast. They characterized the heterogeneity of translation initiation mediated by GCN4-5'UTR using different techniques and found a subpopulation of cells that consistently exhibited enhanced GCN4 translation under non-starvation conditions.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Acoustics
Kalman Klapcsik, Ferenc Hegedus
Summary: This study compares the accuracies of two numerical approaches used to model the translational motion of an acoustic cavitational bubble in a standing acoustic field. The first approach decouples the equation of translational motion from the radial oscillation, while the second approach solves the coupled ordinary differential equations directly. Results show that both models can reveal stable equilibrium positions, but the time-resolved approach provides more accurate results in oscillatory solutions where transient behavior is important.
ULTRASONICS SONOCHEMISTRY
(2023)
Article
Microbiology
Giuseppe Cimicata, Gil Fridkin, Tanaya Bose, Zohar Eyal, Yehuda Halfon, Elinor Breiner-Goldstein, Tara Fox, Ella Zimmerman, Anat Bashan, Natalia de Val, Alexander Wlodawer, Ada Yonath
Summary: This study used cryo-EM techniques to image ribosomes from Staphylococcus aureus and identified a previously unobserved conformation. The findings shed light on the mechanism and significance of the helix 68 in the protein synthesis process.
Article
Biochemistry & Molecular Biology
Gideon K. Gogovi, Swabir Silayi, Amarda Shehu
Summary: The study examines the structural dynamics and energetic properties of a C-terminal domain of the Rift Valley Fever Virus L protein solvated in glycerol and aqueous glycerol solutions in different concentrations using all-atom molecular dynamics. It is found that peptide helices and sheets are maintained only when the modeling strategy considers the solvent with lower glycerol concentration, and that solvent-peptide interaction becomes more cohesive with decreasing glycerol concentrations. The density and radial distribution function of glycerol solvent calculated with modified atomic charges show good agreement with experimental results and other simulations at 298.15K.
Article
Biochemistry & Molecular Biology
Hanna Kratzat, Timur Mackens-Kiani, Michael Ameismeier, Mia Potocnjak, Jingdong Cheng, Estelle Dacheux, Abdelkader Namane, Otto Berninghausen, Franz Herzog, Micheline Fromont-Racine, Thomas Becker, Roland Beckmann
Summary: In eukaryotic translation, the termination and ribosome recycling phases are linked to the initiation of a new round of translation by factors such as ABCE1 and eIF3j. Cryo-EM analysis of native yeast and human ABCE1-containing pre-initiation complexes revealed their association with 43S and 48S initiation phases, showcasing a novel hybrid conformation and interaction network. This study provides valuable insights into the structural and functional roles of ABCE1 and eIF3j in translation initiation.
Article
Materials Science, Multidisciplinary
A. Samartzis, S. Chillal, A. T. M. N. Islam, K. Siemensmeyer, K. Prokes, D. J. Voneshen, A. Senyshyn, D. Khalyavin, B. Lake
Summary: The quantum magnet BaCuTe2O6 exhibits a complex magnetic network in a cubic crystal structure. Antiferromagnetic interactions are present with a Curie-Weiss temperature of approximately -33 K, leading to long-range magnetic order at around 6.3 K. The magnetic structure reveals antiferromagnetic order along chains parallel to the crystal axes, with a consistent intrachain interaction value of about 34 K. Additionally, a weaker antiferromagnetic, frustrated hyperkagome interaction couples the chains in a noncollinear arrangement.
Article
Acoustics
Xun Wang, Weizhong Chen, Min Zhou, Zekun Zhang, Lingling Zhang
Summary: This paper investigates the pulsations and translation of bubbles in a double-bubble system driven by burst ultrasound. The results show that adjusting the burst frequency and amplitude can enhance the pulsations and improve the translation velocities of bubbles. Larger bubbles result in faster translation velocities, but the velocity decreases for excessively large bubbles. The initial distance between bubbles also affects the translation velocities.
ULTRASONICS SONOCHEMISTRY
(2022)
Article
Chemistry, Physical
Thomas E. E. Tsangaris, Spencer Smyth, Gregory-Neal W. Gomes, Zi Hao Liu, Moses Milchberg, Alaji Bah, Gregory A. A. Wasney, Julie D. D. Forman-Kay, Claudiu C. C. Gradinaru
Summary: The intrinsically disordered protein 4E-BP2 interacts with eIF4E to regulate mRNA translation. Phosphorylation of 4E-BP2 reduces its binding to eIF4E. This study generated structural models of 4E-BP2 in different phosphorylation states and validated them using experimental data. The results provide insights into the interplay between different regions of 4E-BP2 and the effects of phosphorylation on these interactions.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Multidisciplinary Sciences
Lulu Guo, Jie Cheng, Shuo Lian, Qun Liu, Yan Lu, Yuan Zheng, Kongkai Zhu, Minghui Zhang, Yalei Kong, Chao Zhang, Naikang Rong, Yuming Zhuang, Guoxing Fang, Jingjing Jiang, Tianyao Zhang, Xiang Han, Zili Liu, Ming Xia, Shangming Liu, Lei Zhang, Stephen D. Liberles, Xiao Yu, Yunfei Xu, Fan Yang, Qian Li, Jin-Peng Sun
Summary: Odorants are detected as smell in the nasal epithelium of mammals by two G-protein-coupled receptor families. In this study, the cryo-electron microscopy structures of mouse TAAR9 (mTAAR9) and its complexes with different odorants were determined. The structures reveal important features for amine odorant recognition, receptor activation, and G protein coupling. This study provides a structural basis for understanding odorant detection and olfactory receptor activation.
