protein folding

Molecular Consequences and Targeting of PPM1D Overexpression in Myeloproliferative Neoplasms.

Phosphatase Mg2+/Mn2+ dependent 1D protein (PPM1D) is a serine threonine phosphatase known to regulate oncogenic pathways. PPM1D mutations are enriched in therapy-related MDS and AML, but the role of PPM1D in myeloproliferative neoplasms (MPN) remains largely unexplored. By sequencing 519 MPN patients, we detected acti...

Encapsulation-Activated Deep-NIR Triarylmethane Dyes via Steric Hindrance Engineering for Long-Circulating Fluorescence/Photoacoustic Dual-Modal Bioimaging

NIR-II fluorescence/photoacoustic dual-modal imaging offers complementary advantages in sensitivity and penetration depth. However, its efficacy is compromised by aggregation, nonspecific binding, and background interference, which persist even with polymeric encapsulation. To address these limitations, we report her...

Testing mean-pooled protein language model target embeddings beyond target identity in drug-label adverse drug reaction annotation: a preregistered controlled representation study

Code, frozen specifications, confirmatory out-of-fold predictions, derived data and transparency records for the preregistered v3 study (PLOS ONE submission). Code: MIT (LICENSE) Data, predictions, results and records: CC BY-SA 4.0 (LICENSE-DATA.md) Citation metadata: CITATION.cff Masked transparency records: see maski...

Engineering a stable high-copy episomal plasmid in Yarrowia lipolytica.

Episomal plasmids are widely used in yeast metabolic engineering for their flexibility and high transformation efficiency. However, their application in Yarrowia lipolytica is often limited by low copy number and insufficient genetic stability. In this study, a robust episomal plasmid that balanced genetic stability an...

Session 5: Proteostasis Mechanisms: Protein Folding and Degradation (joint session)

Brazil Nut–Yellow Pea Hybrid Plant-Protein Beverages Subjected to UHT Processing: Protein Colloidal Stability during Production and Storage

Proteins from legumes and nuts are important allies for formulating animal-free products with a well-balanced amino acid profile. However, limited information is available on their behavior during food processing. Thus, the colloidal stability of hybrid plant-based UHT-processed beverages containing yellow pea and Br...

Modulation of Electrophysiology and Plaque Aggregation in Huntington’s Disease Patient-Derived Cells by Picosecond Pulsed Electric Fields

Huntington’s Disease (HD) is a fatal, autosomal dominant neurodegenerative disorder characterized by progressive motor and cognitive decline. Unstable expansion of cytosine-adenine-guanine (CAG) trinucleotide repeats in the huntingtin gene, often exceeding 35–40 repeats, results in an extended polyglutamine (PolyQ) tra...

A Human ABCG2 SNP Variant, P269S (rs34678167, c.805C>T), Increases Cellular Resistance to Mitoxantrone and SN-38 Without Detectable Differences in ABCG2 Abundance in Total and Biotinylated Protein Fractions

ABCG2 (BCRP/MXR) is an ATP-binding cassette transporter that plays a role in cellular resistance to various anticancer agents. While several non-synonymous single-nucleotide polymorphisms (SNPs) in the ABCG2 gene have been functionally characterized, the effects of many variants remain uncertain. This study examined th...

Per-Stage Controls and Failure Modes in a Co-Folding Virtual Screening Cascade for the Keap1–Nrf2 Interaction

Virtual-screening cascades combine learned affinity prediction, co-folding, physics-based rescoring and molecular dynamics, but each score requires an independent control. We audited these stages for the Kelch-like ECH-associated protein 1 (Keap1)–nuclear factor erythroid 2-related factor 2 (Nrf2) interaction using a 1...

Beyond Stochastic AI: The V3 Deterministic Superintelligence Framework via Formal Verification, Causal Invariants, and DO-178C DAL-A Compliance

ABSTRACT The current paradigm of artificial intelligence is dominated by stochastic models—large language models, neural networks, and reinforcement learning systems—that are powerful yet fundamentally unpredictable, susceptible to hallucinations, drift, and adversarial manipulation. Conventional safety mechanisms (RLH...

Systematic Screening of Reference Genes for qPCR in Procambarus clarkii: RPL13a Shows Stable Expression Under Non-Ionic Ammonia Stress and Multiple Experimental Conditions

Real-time quantitative PCR (qPCR) is a key technique for elucidating the mechanisms underlying environmental stress responses in aquatic animals, and its accuracy relies heavily on stable reference genes for data normalization. In this study, histopathological examination revealed alterations in the gill, hepatopancrea...

An Integrative Machine Learning Framework for Drug Repurposing Using Molecular Docking and Drug Sentiment Analysis in Type 2 Diabetes

Type 2 diabetes (T2D) is a major global health challenge that requires continuous investigation of alternative therapeutic strategies. Drug repurposing is a strategic technique that involves identifying new therapeutic applications from existing drugs. This research developed a machine learning framework that combine...