RNA and protein synthesis mechanisms

PARSEbp improves RNA structure scoring by integrating pairwise agreement and base pairing consistency, outperforming existing methods on CASP16 targets.

The paper identifies uORFs in bacterial mRNAs using bioinformatics and experimental validation, revealing translational coupling and ribosome-mediated RBS occlusion as regulatory mechanisms.

This study investigates solvation dynamics in two viral RNAs, revealing how RNA conformational flexibility and protein binding influence hydration and ion reorganization.

The paper introduces a framework to identify RNA triple helices using secondary structure data, achieving high precision and accuracy in detecting known triple-helix motifs.

The paper develops a machine learning method to optimize coding sequences for improved protein expression in mammalian cells by analyzing synonymous codon effects.

This study examines codon usage differences between host-specific rabies virus clades and identifies non-GC3 nucleotide content as a key driver of these differences.

RTM-align improves RNA structure alignment by addressing size dependency and short fragment handling, outperforming existing tools in accuracy and reliability.

This study characterizes RlaP family nucleotidyltransferases from Pseudomonas species, showing they repair damaged RNAs by adding nucleotides and are essential for RNA function restoration.

This study shows linear mRNAs can undergo backward translation in vitro, producing signals comparable to forward translation, and demonstrates the potential of backward translation in synthetic biology.

The paper identifies missing steps in mitochondrial translation initiation in plants using cryogenic electron microscopy.

The paper describes a Kaggle competition for RNA 3D structure prediction, showing that template-based methods can outperform deep learning approaches.

The paper shows that nascent polypeptide feedback triggers ribosomal frameshifting and transcript decay through specific motifs and splicing events.

This study shows chronic stress prevents stress granule formation in response to acute stress by causing ribosome stalling and partial polysome preservation.

This paper introduces OPENER, an engineered eRF1 variant that suppresses nonsense mutations and enables nonstandard amino acid incorporation, showing therapeutic benefits in a Duchenne muscular dystrophy model.

The paper introduces mRNA-GPT, a generative mRNA language model trained on sequences from bacteria, eukaryotes, and archaea, showing improved translation efficiency and stability in mRNA design.

The paper introduces a measurement framework to characterize cell-free expression systems by analyzing transcription and translation dynamics using nucleic acid templates and Escherichia coli extracts.

This study investigates how two structurally similar ligands, 4EGI-1 and i4EG-BiP, regulate eIF4E through distinct binding modes, revealing that frontal binding promotes 4E-BP1 over eIF4G interaction.

This study develops an orthogonal translation initiation system using an i-tRNA-AAC mutant and evaluates its physiological impact through fluorescence assays, proteomics, and tRNA sequencing.

This study identifies NAC's role in regulating translation elongation, cotranslational folding, and organelle targeting through sequence-specific interactions with nascent polypeptides.

This study identifies montanine as a potent antiviral compound that inhibits RNA viruses by targeting translational elongation and GCN1-related stress responses.

This study shows that codon usage changes with longevity in mammals, with some codons favoring optimal translation and others slowing translation to aid protein folding, contributing to proteostasis and reduced aging.

The paper demonstrates that ACE-tRNAs enable readthrough of COL4A5 nonsense variants, restoring full-length protein expression and heterotrimer formation in cell models of Alport syndrome.

The paper designs RNA switches using Restricted Boltzmann machines and validates their structural switching properties through experimental testing.

The paper demonstrates that the PURE cell-free system can be reconstituted from non-ribosomal proteins synthesized by the system itself.

fpocketR identifies and analyzes ligand-binding pockets in RNA structures to discover potential drug targets.

The paper profiles the proteome and phosphoproteome of yeast expressing three mistranslating tRNA variants, showing varied growth defects and impacts on cellular processes.

The paper identifies translational repression of 5' TOP mRNAs in exhausted human CD8+ T cells despite elevated mTOR activity.

The paper identifies the prevalence and structural contexts of dual-donating amines in structured RNAs using computational analysis of RNA structures.

This study investigates the structural and dynamic differences between substrate and intermediate states of Mtb MetRS, revealing how mutations affect enzyme stability and activity.

The paper introduces an efficient RNA folding model that accurately simulates RNA hairpin unfolding and reproduces experimental thermodynamic properties.