RNA and protein synthesis mechanisms

This study reveals how TACO1 enhances mitochondrial translation efficiency by stabilizing tRNA and promoting ribosomal translocation, with implications for bacterial orthologs.

The paper investigates the evolutionary and functional roles of translation initiation factor 2 (IF2) terminal extensions across bacteria, showing their role in stress response and adaptation.

This study shows enteroviruses can use two upstream AUGs for translation initiation, with the second AUG providing a competitive advantage in specific host environments.

This study presents cryo-EM structures of a circularly permuted group II intron, revealing the mechanism of the hydrolysis pathway and its regulation by branch point and splice site mutations.

This study investigates the evolutionary remodelling of isoleucyl-tRNA synthetase C-terminal domains in prokaryotes, finding that such remodelling enhances aminoacylation rates.

The paper introduces Dashing Turtle (DT), an algorithm for high-resolution detection of RNA structural modifications using direct RNA nanopore sequencing, showing improved accuracy over existing methods.

Cat_Wiz corrects and annotates Mg2+ ion binding sites in RNA structures using stereochemistry-guided tools, improving accuracy and enabling machine learning applications.

This study develops reversible RNA acylating reagents using a nitro reduction strategy and demonstrates their ability to modulate RNA function and translational activity in vitro and in cells.

This study compares Dictyostelium discoideum 3'-5' RNA polymerases, identifying a conserved residue with dual roles in catalysis and substrate specificity.

This study identifies SLFN14 as a ribosome-associated endoribonuclease that represses translation by selectively cleaving type II tRNAs, and shows how mutations linked to thrombocytopenia disrupt this mechanism.

The paper uses Bayesian Markov models to explain asymmetric ATP hydrolysis kinetics in ABCE1 without requiring direct cooperativity between nucleotide-binding sites.

The paper identifies and classifies 163 putative Type IV IRESs from diverse viruses, revealing structural variations that correlate with functional differences.

This study shows that eIF5B is crucial for OSCC cell survival by enabling non-canonical translation of pro-survival mRNAs, and its inhibition reduces tumor growth and sensitizes cells to apoptosis.

gCoSRNA predicts coaxial stacking in RNA junctions using sequence and secondary structure, achieving high accuracy across multiple branch types.

The paper shows that slow translation elongation reduces protein output per mRNA, independent of mRNA stability, and demonstrates a dynamic balance between initiation and elongation rates.

RNAnneal predicts RNA structural ensembles using deep learning and physics-based modeling, outperforming existing methods in classifying experimentally resolved conformations.

This study introduces PRIME, a method to measure RNA structural energetics, finding that RNA base pairs and tertiary interactions dynamically open with low-energy fluctuations.

The paper develops an improved method to capture ribosome-associated proteins and shows viral infections remodel these proteins in a virus-specific manner, with functional implications for viral propagation.

Toehold-VISTA designs RNA sensors using machine learning, improving function against SARS-CoV-2 RNA by integrating biophysical modeling and PLS-DA.

This study identifies active transport of tRNAs via endolysosomal vesicles in large cells, showing that LeuRS facilitates this process and its disruption impairs protein synthesis and cell size.

This paper introduces a hierarchical method for predicting RNA pseudoknots by analyzing local energy gains between sections of unpaired bases, showing high accuracy and computational efficiency.

The paper defines functional gene families in S. cerevisiae by analyzing codon usage patterns using a new statistical method called ASCS.

This study identifies ZNF598 as a factor resolving translation stress during metabolic adaptation, showing its role in mitochondrial biogenesis and metabolic flexibility.

mRNAfold improves mRNA design by co-optimizing stability, local structure, and codon choice, showing better in-solution stability and complex effects on protein production.

This study uses all-atom simulations to analyze nucleotide-nucleotide and nucleotide-amino acid interactions, revealing key binding modes and their role in biomolecular condensate formation.

The paper investigates the StopGo/2A translational recoding mechanism using cryo-EM and bioinformatics, revealing structural and sequence features that enable this process in viruses.

The paper investigates a disease-causing mutation in IARS1 that affects protein complex formation and the integrated stress response, leading to altered cellular stress responses.

This study identifies a PrfH subfamily that rescues both damaged and intact ribosomes stalled in translation, revealing dual mechanisms for peptide hydrolysis.

This study shows that 5' UTR length influences alternative N-terminal protein isoform production through start codon selection and demonstrates this in health and disease.

QuAPPro is an R/shiny app for quantifying and aligning polysome profiles, enabling interactive analysis of UV absorbance and fluorescence data from polysome profiling experiments.