protein folding

Epigallocatechin-3-Gallate Restores the Pulmonary Keap1-Nrf2-HO-1 Pathway and Attenuates Bile Acid-Associated Lung Injury in a Mouse Model of MASH

The crosstalk between the liver and the lung is complex and not yet fully understood; however, recent studies suggest that metabolic dysfunction, often originating in the liver, can influence lung injury and other lung diseases. The current study investigates the role of bile acids (BA) in mediating lung injury in a mo...

Anneal-MaxCal: kinetic ensembles from a Markov model learned along a solute-tempering ladder

A full characterisation of a molecular system requires its metastable states, their populations and their interconversion rates. Molecular Dynamics can in principle provide this characterisation but is limited by sampling and by force-field inaccuracies. Enhanced sampling addresses the first problem, but typically requ...

Oxidative Stress-Related Prognostic Signature Defines Redox Adaptation and Immune Remodeling in Triple-Negative Breast Cancer

Triple-negative breast cancer (TNBC) is an aggressive and molecularly heterogeneous breast cancer subtype. We developed a six-gene oxidative stress-related signature (BAG5, ANXA2, LONP1, GBE1, CBR1, and DDIT4) in GSE58812 (107 patients; 29 deaths) and evaluated its transportability in GSE21653 (83 TNBC patients; 25 dis...

Direct monitoring of unfolded nascent polypeptides by the CCR4-NOT complex contributes to protein quality control through selective mRNA deadenylation and decay

Accumulation of aberrant and unfolded proteins induce cellular stresses and contributes in human to diseases and aging. Several cellular pathways combat the formation of these deleterious molecules. Recently, processes limiting the production of unwanted polypeptides through the co-translational degradation of their me...

esm2-layer-invariance: depth matters but the final layer suffices - leakage-free evaluation of layer choice in protein language models (BIOINF-2026-2348 second revision)

Code and per-dataset results for the second revision of manuscript BIOINF-2026-2348 (Bioinformatics). This version adds: (1) the unified-protocol pooling contrast between the random and leakage-free splits with per-dataset paired bootstrap statistics; (2) published ProteinGym v1.3 anchors recomputed per assay on the sa...

Applying super-resolution microscopy to detect mitochondria-endoplasmic reticulum contact sites

Membrane contact sites (MCS) are regions in the cell where the membranes of two organelles come into close proximity without fusing. Contact sites between mitochondria and the endoplasmic reticulum (MERCs) are arguably the most well-studied MCS. The study of MERCs is commonly conducted using fluorescence colocalization...

AncientProteinScripts

Code accompanying the paper "Ancient amino acid sets enable stable protein folds" (Giacobelli, Andersson, et al., bioRxiv 2025, doi:10.1101/2025.10.29.685319). Contents: Protein design pipeline: RFdiffusion backbones, ProteinMPNN sequences restricted to a 10-amino-acid ancient alphabet, and a 20-amino-acid comparison d...

Antioxidant Activity, Carbohydrate‐Hydrolysing Enzyme Inhibition, Antihyperglycaemic Effect and Associated Expression Changes of Bryophyllum pinnatum ‐Fortified Wheat‐Plantain Snack in Streptozotocin‐Induced Diabetic Rats

Type 2 diabetes is a risk factor for cardiovascular morbidity and mortality. Sugar‐laden snacks have been implicated as one of the major contributors when consumed in excess. The development of new snack products enriched with value‐added bioactive properties can open up fresh opportunities for health‐conscious con...

Iron exposure reprograms redox homeostasis through mitochondrial depolarization in neuroblastoma

Purpose. Neuroblastoma is the most common malignancy of infancy, and cancer cells strongly depend on iron metabolism for proliferation. Whether sub-cytotoxic iron load reprograms mitochondrial and redox metabolism, and how this relates to the malignant behavior of neuroblastoma cells, is poorly defined. We hypothesized...

Frustration Quenching and Network Topology of the Energy Landscape as Primary Determinants of Protein–Ligand Binding Pose Prediction by Deep Learning Models

Deep learning co-folding and docking models accurately predict ligand binding poses at orthosteric sites yet systematically underperform at allosteric pockets. Here, we demonstrate that this accuracy gap reflects a fundamental biophysical property of local energy landscape topology specifically, the magnitude of frustr...

Two-step purification and characterization of chitinase from Bacillus cereus V5331: evaluation of antagonistic potential of enzyme against fruit juice contaminant Saccharomyces cerevisiae

Chitinases are gaining importance as biocatalysts for environmentally friendly food preservation and biocontrol. The present study reports on the purification and biochemical characterization of a chitinase from Bacillus cereus V5331 and its anti-yeast activity in grape juice. The enzyme was purified by Sephadex G-100,...

Solution fold of HIV-1 Virus protein U cytoplasmic domain in the presence of DPC micelles