protein folding

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

Soil Protists Consume Viruses to Drive Microbial Nutrient Cycling: Overlooked Trophic Pathways in Soil Food Web

Soil viruses are traditional top-down regulators that redistribute organic matter through host lysis and the viral shunt, implicitly positioning them as terminal sinks rather than active trophic components. Here, we show, for the first time, that soil viruses can also be direct prey for protists, establishing an over...

On the Structural Precision Required for Ligand-Specific Elastic Network Dynamics of AI Co-Folded GPCR Structures

Background/Objectives: AI-based protein–ligand co-folding methods such as Boltz-2 are able to reproduce experimentally determined ligand binding poses at G protein-coupled receptors (GPCRs) with increasing accuracy and precision. As these models advance, they raise several natural questions: assuming the correct placem...

The bromodomain and its contribution to human health

ReCAST: Single-Cell-Informed Tumour Microenvironment Profiling for Translational Prognostic Assessment in Esophageal Cancer

Background/Objectives: Single-cell transcriptomics provides detailed maps of the tumour microenvironment, but translating these maps to large clinical cohorts requires methods that can recover biologically meaningful cell states from routinely available bulk transcriptomes and establish whether these states provide inf...

Integrated Strategy for Sustainable Outdoor Photo-Fermentative Biohydrogen Production: Sequential Optimization, Repeated-Batch Operation, Modular Bioreactor Simulation, and Biomass Valorization

This study developed an integrated strategy for outdoor photo-fermentative biohydrogen production by Rhodopseudomonas pentothenatexigens KKU-SN1/1 through low-cost medium optimization, repeated-batch operation, modular bioreactor simulation, and biomass valorization. A sequential experimental design combining one-facto...