RNA and protein synthesis mechanisms

This paper develops a coarse-grained RNA model (iConRNA) with explicit Mg2+ to simulate RNA phase separation and reveals the role of RNA folding and ion interactions in driving phase transitions.

This study uses smFRET and MD simulations to reveal the dynamic conformational changes of the guanidine-III riboswitch, showing how Mg2+ and ligand binding stabilize and trap its folded state.

This study investigates how herpesvirus ubiquitin deconjugases counteract ribosomal quality control responses during translational stress, revealing differences in their effectiveness across virus types.

The paper shows that virus propagation can occur through low-level host protein variants caused by gene-expression errors, using bacteriophage T7 and thioredoxin as a model.

This study uses single-molecule techniques to analyze tRNA selection during eukaryotic translation, revealing faster near-cognate sampling and a negative correlation between near-cognate concentration and tRNA accommodation efficiency.

This paper develops a chemical probing strategy using preQ1 and its riboswitch RNA to study RNA-small molecule interactions in living bacteria, mapping binding sites through mutational profiling.

This study investigates the substrate specificity of the PEARL BhaBCAla, showing it can use non-cognate amino acids and tRNAs for peptide extension, with efficiency depending on both amino acid and tRNA features.

This study designs a covalent small molecule targeting unpaired guanines in a riboswitch, showing it modulates riboswitch function in a cellular reporter system.

This study characterizes the effects of three small-molecule inhibitors on MtbRNAP transcription elongation using optical tweezers, revealing distinct inhibition mechanisms and synergistic effects.

RNAtranslator generates RNA sequences that bind to specific proteins by treating RNA design as a sequence-to-sequence translation task, producing novel and high-affinity sequences.

The paper shows heat shock increases silent ribosomes and reorganizes mRNA turnover in yeast by prioritizing heat-shock protein synthesis over ribosome biogenesis.

The paper identifies primate-specific motifs in human rRNAs and 45S spacers that are also found in nervous system genes linked to disorders like autism and schizophrenia.

This paper introduces CaCoFold-R3D, a method that jointly predicts RNA 3D motifs and secondary structure using evolutionary information, demonstrating its effectiveness for RNA structure prediction.

This study uses RCP-seq to analyze translation initiation dynamics in mouse brain tissues, revealing SSU poising and uORF effects on translational efficiency.

The paper presents a platform for biosynthesizing aromatic noncanonical amino acids in E. coli and incorporating them into proteins using orthogonal translation systems.

This study examines the Central Dogma in Arabidopsis thaliana, showing that codon frequencies and mRNA levels are better predictors of protein expression than methylation, tRNA, or ribosome-associated transcripts.

This study shows that BCAA starvation causes codon-specific ribosome stalling, affecting translational dynamics and protein output in mammalian cells.

This study identifies PARP10 as essential for stress granule initiation, showing it regulates assembly kinetics and modifies G3BP1 to influence SG composition.

The paper analyzes frameshifts in tandem repeats across proteomes, showing they significantly alter protein physicochemical properties and function.

This paper uses large language models and active learning to optimize cell-free protein synthesis, achieving significant yield improvements for antimicrobial proteins.

This study investigates mRNA translation dynamics during mouse pre-implantation development, revealing novel mechanisms of translational selectivity and the role of Eif1ad3 in ribosome biogenesis.

The paper identifies eIF1A and eIF5B as repressors of C9orf72-mediated RAN translation by showing their omission enhances RAN translation in all reading frames.

This paper develops a system for controlling in vitro DNA replication using genetically encoded circuits and demonstrates its replication and repression capabilities.

The paper investigates how the human ribosome modulates multidomain protein folding by delaying domain docking, contrasting with bacterial ribosomes.

This study uses computer simulations to reveal the conformational pathways of a T-box riboswitch in recognizing tRNA, showing three thermodynamic states and their dependence on Mg2+ concentration, with implications for antibiotic development.

This study investigates the RNA-binding mechanism of ProQ using molecular dynamics simulations, revealing electrostatic interactions and structural changes upon raiZ RNA binding.

This study investigates how auxiliary information improves RNA secondary structure prediction accuracy by analyzing suboptimal structures and using topological data analysis features.

This study maps oxidative and nitrosative damage to ribosomal RNA in human cells under stress, revealing distinct damage patterns in cytosolic and mitochondrial ribosomes.

The paper identifies a ribosomal mutation conferring cycloheximide resistance in C. elegans and shows it alters translation efficiency and developmental timing without activating stress pathways.

This study uses RNA-seq and Ribo-seq in Haloferax volcanii to identify genes and small RNAs with altered translation during oxidative stress, revealing new regulatory mechanisms.