protein folding & dynamics

Phosphorylation-dependent conformational change in the Keratin 19 head domain: Implications for filament assembly and binding to GSK3β and 14-3-3

This study identifies a phosphorylation-dependent conformational change in the K19 head domain that affects filament assembly and interactions with GSK3β, but not 14-3-3 proteins.

Bioinformatic pipeline for functional inference of Rickettsia akari hypothetical proteins reveals virulence-associated and effector candidates

The paper uses a bioinformatic pipeline to analyze hypothetical proteins in Rickettsia akari, identifying candidates with potential roles in virulence and host interaction.

Rapid generation of antibody conformational ensembles using machine learning

This paper introduces Cadense, a machine learning framework that generates antibody conformational ensembles from sequence, capturing dynamic properties and improving docking accuracy.

MaaD-TAD: an all-atom model of the duplicated PRAMEF/HNRNPCL chromatin domain built from sequence homology

The paper introduces MaaD-TAD, an all-atom model of a duplicated chromatin domain, using sequence homology and cohesin placement to reconstruct DNA structure where Hi-C data are missing.

Skeletal muscle aging drives sex- and compartment-specific protein insolubility that is modifiable by proteostasis-directed treatments

This study investigates age-related changes in protein insolubility in skeletal muscle and shows that these changes are sex- and compartment-specific and can be modified by exercise and rapamycin.

Amino acid clustering and epistasis guide sequence-based prediction of phenotype modulation

The paper develops a method to predict phenotype modulation by analyzing amino acid clustering and epistasis in protein sequences, showing that these factors improve prediction accuracy.

Multi-Enzyme Data-Independent Acquisition Mass Spectrometry for Proteoform-Aware Single-shot Proteomics

The paper introduces mE-DIA, a multi-enzyme DIA-MS workflow that improves proteoform detection in proteomics by integrating analysis and interpretation into a single toolset.

LinearKnot: linear-time ensemble analysis of RNA density-2 pseudoknots under hierarchical folding

LinearKnot approximates CParty's hierarchical pseudoknot analysis with linear time complexity, achieving comparable accuracy for RNA structure prediction and ensemble calculations.

Programmable interphyla communication for Staphylococcus aureus by transferability of homoserine lactone sensors between Bacillales bacteria

This study demonstrates the transferability of homoserine lactone sensors between Bacillales bacteria, enabling programmable interphyla communication between Gram-negative and Gram-positive species.

Developmentally-regulated splice remodeling shapes functional CACNA1C channel diversity during human neurodevelopment

This study identifies developmentally-regulated alternative splicing of CACNA1C during human neurodevelopment and shows it affects CaV1.2 channel function.

Integrated Transcriptomic and Translatomic Profiling Reveals Noncanonical RNA Junctions and Hidden Coding Potential in Porcine Epidemic Diarrhea Virus

This study identifies noncanonical RNA junctions and hidden coding potential in PEDV using integrated transcriptomic and translatomic approaches.

Vasopressin V2 receptor phosphopeptide reshapes the conformational landscape of arrestin-2 beyond C-tail detachment

The paper uses simulations to show that V2Rpp binding broadens the conformational landscape of arrestin-2 beyond C-tail detachment, with interdomain rotation angles being less favored without V2Rpp.

Redox regulation of 2-carboxy-D-arabinitol 1-phosphate phosphatase in Fabaceae is associated with high Rubisco dark inhibition

The paper identifies a conserved cysteine pair motif in CA1Pase linked to redox regulation and inhibitor degradation in Fabaceae species.

Decoupling Quantification and Identification for Label-Free Top-Down Proteomics Improves Proteome Coverage

This paper introduces a workflow that decouples quantification and identification in label-free top-down proteomics, improving proteome coverage and quantification precision.

The yeast Gcn2 protein kinase mediates P-body formation both through its activity with eIF2α and with non-canonical substrates

This study shows that yeast Gcn2 promotes P-body formation through eIF2α phosphorylation and Smu2-dependent mRNA granule maturation, even when eIF2α phosphorylation is blocked.

PP271, a novel bacteriophage primase-polymerase, enables Primer-Free DNA Amplification

This paper characterizes PP271, a novel bacteriophage PrimPol enzyme, showing it can synthesize DNA primers that are efficiently extended by Phi29 DNA polymerase for primer-free amplification.

Inter-domain flexibility in F-Box proteins revealed by integrative modeling

The paper uses integrative modeling to reveal inter-domain flexibility in F-box proteins, showing varying conformational dynamics across different F-box proteins.

PyTorch Frustratometer: An Ultra-fast, Parallelized Tool for Proteome-Scale Local Energetic Frustration Analysis

The paper introduces a PyTorch-based tool for fast proteome-scale local frustration analysis, achieving 70-13,000x speedup over the original FrustratometeR.

Glycine-Proline driven flexibility and interface-dependent conservation of six-residue {Omega}-loops in protein complexes

The paper analyzes six-residue Omega-loops in protein complexes, showing their structural constraints, sequence conservation patterns, and functional significance through sequence design and mutation mapping.

Frequency-Dependent Structural Responses of Amyloid-β Fibrils to Terahertz Pulses: A Nonequilibrium Molecular Dynamics Study

This study uses nonequilibrium molecular dynamics to show frequency-dependent structural changes in amyloid fibrils under terahertz pulses, identifying two electric-field thresholds for disruption.

Massive inter-animal horizontal gene transfer contributes to stress tolerance in the fungus gnat Bradysia coprophila

This study identifies extensive horizontal gene transfer in the fungus gnat Bradysia coprophila, showing these genes contribute to stress tolerance and ecological adaptation.

Mutant Isocitrate Dehydrogenase 1 Alters Extracellular Vesicle Secretion and Cargo Composition in Cellular Models

This study shows mutant IDH1 increases sEV secretion and alters their cargo composition in glioma and chondrosarcoma cells, with D2HG packaged into sEVs and cell-type-specific cargo remodeling.

Endothelial protein C receptor is an entry receptor for Langya virus

This study identifies the endothelial protein C receptor (EPCR) as the entry receptor for Langya virus and reveals the molecular basis of its interaction with the viral attachment glycoprotein.

Multimodal cellular context enables molecular phenotyping from single-molecule trajectories

The paper introduces MIST, a framework that integrates single-molecule trajectory data with cellular context to improve molecular phenotyping in E. coli.

PARP1-mediated PARylation of SPRTN restrains its DNA-protein crosslink repair activity

This study shows PARP1-mediated PARylation of SPRTN limits its DNA-protein crosslink repair activity by reducing DNA binding and proteolytic function.

Predicting the alternative conformation of a known protein structure based on the distance map of AlphaFold2

This study shows that AlphaFold2 distance maps can reveal multi-state protein structures, enabling prediction of alternative conformations with high accuracy.

Amyloid stability and condensate material properties independently govern the hnRNPA2 condensate to fibril transition

This study shows that amyloid structure and condensate stability independently influence the hnRNPA2 condensate-to-fibril transition, revealing a structural framework for this process.

Onsite fixation preserves phosphoprotein profile in human whole blood

This study shows that fixing whole blood at collection preserves phosphoprotein profiles, particularly in neutrophils and monocytes, better than cryopreserved PBMCs.

Charting the Structure and Functional Landscape of the SF3B1 Intrinsically Disordered Region

This study characterizes the conformational dynamics and phosphorylation-dependent changes in the SF3B1 N-terminal domain using a combination of biophysical and computational methods.

Unraveling Systemic Responses to NQO1-Activated IB-DNQand Rucaparib Single and Dual Agent Therapy in Triple-Negative Breast Cancers

This study evaluates the effects of IB-DNQ and Rucaparib on TNBC cells, revealing synergistic effects and novel protein biophysical changes via thermal proteome profiling.