protein folding

Resolving Heterogeneous Mechanical Domains via Physics-Aware Deep Clustering of Single-Molecule Force Spectroscopy Data

Many biological processes rely on mechanical forces, with protein molecules acting as key mediators. Understanding how proteins respond to mechanical stress is essential for conditions including cardiomyopathy and muscular dystrophy. Natural proteins such as dystrophin and utrophin are composed of heterogeneous folding...

Alterations of the Saccharomyces cerevisiae proteome by protein production are dependent on strain origins

Abstract Saccharomyces cerevisiae yeast is a widely used recombinant protein production host. Recombinant protein expression requires adaptation of the host cell proteome to accommodate the increased biosynthetic and folding demands. However, this underlying proteomic changes remain poorly understood. In this study, we...

Micro-vascularized Multicellular Pancreatic Ductal Adenocarcinoma (PDAC) spheroid: A novel 3D PDAC Research Model.

This model enables analysis of tumor-endothelial-stromal interactions in a pancreas-derived dECM environment and supported PDAC spheroid formation and the CD44-associated endothelial phenotype.

Explainable attention-based multi-omics fusion with protein language models for CML-versus-control classification and biomarker discovery

Chronic Myeloid Leukemia (CML) is a well-defined hematological malignancy driven principally by the BCR::ABL1 fusion oncogene and aberrant tyrosine kinase signaling. Computational methods to predict leukemia suffer from the limitation of using single-modality data or black-box models, which cannot adequately incorporat...

Disentangling folding stability and function in deep mutational scanning fitness

This repository accompanies a computational analysis decomposing protein variant fitness into folding-stability and function components across 151 deep mutational scanning (DMS) assays from ProteinGym. For each assay, the agreement of every predictor with measured fitness was quantified, structure- and sequence-based s...

Exposure of cells to prions induces prion strain dependent changes in mitochondrial redox state and respiration.

During initial prion infection, PrPSc drives mitochondrial dysfunction in a manner that is both strain dependent and independent of PrPC expression, while persistent prion infection increases mitochondrial sensitivity to cellular stress.

Brown and white adipocyte like cells derived exosomes differentially regulate stemness, hormone secretion, apoptosis, and lipid metabolism in model cells

Assessment of the impact of conditioned media or exosomes derived from brown and white adipocyte-like cells on four human cell types highlighted a potential modulatory role of adipocyte-derived exosomes in intercellular communication.

Leveraging Protein Dynamics for Selective Inhibition of Threonyl‐tRNA Synthetase by Obafluorin Analogs

The widespread emergence of antibiotic resistance necessitates the development of novel agents with unique mechanisms of action. Obafluorin (OB), a natural β-lactone antibiotic, is a covalent inhibitor of threonyl-tRNA synthetase (ThrRS), but the high conservation of the active site between prokaryote and eukaryote Thr...

Evolutionary origins of protein novelty across an entire yeast subphylum

A broad computational investigation of genetic and protein novelty throughout the entire subphylum of Saccharomycotina yeasts shows that “invention” of new folds occurs more frequently through de novo emergence, and illustrates cases of evolutionary “re-invention” of existing protein folds from noncoding sequences.

Multicomplex Integrative Structural Modeling of a Human Histone Deacetylase Interactome

Histone Deacetylase (HDAC) 1 and 2 are key enzymatic components in multiple large chromatin remodeling complexes including NuRD, SIN3, and CoREST. In addition, both HDAC 1 and 2 contain a large intrinsically disordered region (IDR) within their C-terminal domain (CTD). How HDAC1/2 assemble into these complexes and the...

Funneliformismosseae symbiosis and TiO2 nanoparticles under drought in Melissa officinalis L.: a machine learning modeling approach

Plant-mycorrhizal symbiosis under combined abiotic stress and nanoparticle exposure remains underexplored. The complexity of such multifactorial systems, combined with the labor-intensive nature of physiology study, challenges conventional analytical approaches. Machine learning can contribute to further elucidating re...

Sodium butyrate improves growth, antioxidant capacity and intestinal health in juvenile common carp fed high-plant-protein diets