protein folding

Label-Free YaxAB Nanopore Fingerprinting of Cancer-Associated Single-Residue Bcl-xL Variants.

Resolving cancer-associated protein variants remains difficult when variants share similar molecular masses and folded structures. Conventional assays often require labels or provide ensemble-averaged readouts, limiting their ability to resolve subtle variant differences. Here, a YaxAB nanopore workflow is presented fo...

ReproBAIT: Can coding agents build their own biological AI tools?

Large language models are increasingly competent at leveraging scientific knowledge and existing computational tools to execute complex workflows. At present, little information exists on their ability to reconstruct tools when given limited descriptions of such tools. We introduce an evaluation titled ReproBAIT (Repro...

Spindle Pole Coupling Failure as a Progressive Driver of Differentiation Suppression in Cancer Initiation

Background: Current cancer initiation models, including multi-hit genomic models and chromosomal instability (CIN) frameworks, do not account for a mechanistically distinct upstream event: progressive protein coupling failure at the spindle pole during mitosis. We propose a novel hypothesis in which coupling failure am...

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

Abstract 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 rep...

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

Abstract 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...

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...