protein folding

Rab Interactions identified by DEEPN.

Rab GTPase Y2H Interactome — Verified Hit DatasetThis dataset contains the curated set of protein-protein interactions identified in a yeast two-hybrid (Y2H) screen against 36 human Rab GTPases, each tested in both nucleotide-locked conformations: GTP-bound (constitutively active, Q→L mutant) and GDP-bound (dominant-ne...

Disease-first public-data integration with local virtual knockout prioritizes shared proteins linking osteoarthritis and osteoporosis

Osteoarthritis and osteoporosis frequently coexist in older adults, but shared molecular programs remain unclear. We developed a disease-first multilayer public-data integration framework to identify shared protein candidates while preserving disease-specific structure before cross-disease comparison. Public bulk trans...

Functional Stability Theory III: Biological Stability and Nash Frustration

A conjectural framework for biological organization spanning molecular to ecosystem scales, organized around thermodynamic game theory and the Maximum Entropy Production Principle (MEPP). The paper examines whether many biological stability problems can be modeled as dissipative structures whose attractors admit Nash-s...

Scalable saturation mutagenesis reveals gene regulatory architecture and rare variant effects

Long-context sequence-to-function models enable nucleotide-resolution prediction of regulatory variant effects, motivating comprehensive mutational interrogation across broad genomic contexts. Yet conventional in silico saturation mutagenesis (ISM) scores mutations one at a time, requiring millions of model evaluations...

Influence of Actinomucor elegans Fermentation on Protein Degradation, Flavor Development, and Nutritional Quality of Tofu

Clinical features associated with macrophage activation syndrome in juvenile dermatomyositis: implications for early recognition

This study aimed to characterize the clinical and laboratory features associated with juvenile dermatomyositis-associated macrophage activation syndrome and to identify warning features that may facilitate recognition of concurrent MAS at JDM presentation. The distribution and potential discriminatory contribution of m...

Responses of the model crop plant Ocimum basilicum L. grown hydroponically to combined hypoxia and salinity

Basil ( Ocimum basilicum L., cv Genovese) cultivated under hydroponic conditions was subjected to salinity, hypoxia, and combined stress for varying lengths of time to assess growth, metabolic, and antioxidant responses. Analyses demonstrated that stress type was the primary factor influencing plant responses, with tre...

Multi-Chain Hamiltonian Replica Exchange Framework for Probing Transient Helices and Order-Disorder Transitions in Proteins

Simulations have emerged as a pillar in biophysics to understand behavior at the molecular scale, in particular for proteins such as intrinsically disordered proteins. These often show transient folding with long-lived states that are challenging to efficiently sample using conventional simulations. Here, we show that...

Peptide-level reanalysis finds a small cleavage shift but no major accessibility bias under osmotic stress

Environmental stress can alter protein folding, molecular interactions, aggregation state, and protease accessibility before proteomic sample preparation. I reanalyzed the publicly available *Yersinia pseudotuberculosis* TMT11plex proteomics data associated with Süer et al. (PNAS, 2026) to test whether the 0.5 M NaCl o...

The bacterial antiphage protein Tiamat is an ATPase and DNase whose homologs are found across the tree of life

Bacteria and archaea encode hundreds of antiviral defense systems, some with homologs found in eukaryotic innate immunity. GHL ATPases like plant MORCs and prokaryotic Tiamat defend against viruses and phage, though their architecture and biochemical activities have remained unclear. Searching thousands of proteomes, w...

Hydrophobic ion pairing as a rational surface engineering strategy for enhanced protein integration within lipid-based nanocarriers

Hydrophobic ion pairing is an established solubility engineering strategy that uses surfactants to modulate drug lipophilicity and facilitate encapsulation in lipid-based nanocarriers. Although promising for enhancing lipophilicity, its influence on protein stability, activity, and interactions with lipids remains uncl...

Deciphering the role of AIM2 in myelin damage and repair in a murine model of multiple sclerosis

Multiple sclerosis (MS) is an immune-mediated disease of the central nervous system (CNS) targeting the myelin sheath and oligodendrocytes. The destruction of either or both myelin sheath or oligodendroglia can lead to the loss of underlying neurones and functional decline in patients. Myelin regeneration is possible i...