protein folding

Association of Body Composition with Tumor Proteomics and Survival in Patients with Clear Cell Renal Cell Carcinoma

Background/Objectives: Prognoses for patients with clear cell renal cell carcinoma (ccRCC) are associated with complex interactions between tumor and patient characteristics. This cross-sectional study investigated associations between body composition and tumor proteomics and their interaction with survival among pati...

A forward genetics platform for papillomavirus research

The inability to perform forward genetics has been a major barrier to human papillomavirus (HPV) research. Here, we report a platform for phenotypic selection of HPV mutants. Our method relies on large “concordant” virus libraries, where each mutant virus particle encapsidates the mutant plasmid that encodes it, thereb...

A phosphoproteome atlas of human cell lines reveals the landscape of kinase activity.

Protein phosphorylation orchestrates cellular signaling and controls most biological processes, with its dysregulation driving diseases, notably cancer. Comprehensive, high-throughput phosphoproteomics remains limited by detection sensitivity, data completeness and computational bottlenecks, especially in low-input set...

Prion-like transmission of human tau strains in the mouse brain

Abstract Most neurodegenerative diseases are thought to spread through the brain by prion-like mechanisms, in which filamentous protein assemblies self-propagate by templated seeding 1 . Distinct conformations of amyloid filaments may provide the physical basis for the strains that lead to different diseases 2 . Howeve...

Directed Evolution of a Protein Catenane Reveals How Noncanonical Topology Modulates Sequence–Property Relationships

Single-domain protein catenanes, in which two mechanically interlocked polypeptide rings fold into a compact structure, provide a tractable system for probing how chemical topology reshapes protein fitness. Using single-domain catenated dihydrofolate reductase (cat-DHFR) as a model, we combined homologue expansion, d...

A conserved molecular signature of electroacupuncture across organs: integrative reanalysis of public transcriptomic datasets

========== 1. RESEARCH QUESTION AND HYPOTHESES ========== Novelty context (verified 2026-09-28 by adversarial literature search): no prior work integrates multiple public acupuncture/electroacupuncture transcriptomic datasets at the raw-data level across organs. Nearest precedents to be cited and differentiated in the...

Beyond Sequence: Propagating Inter-protein Structural Context for Protein Language Models

StrucNS reveals interaction-weighted network topology as the driving predictor of absolute stability of natural and de novo proteins.

StrucNS is a mathematical framework that identifies principles governing protein fitness by employing network science to learn physicochemical relationships between residues and their stability contributions directly from the protein fold, and performs comparably to supervised UniRep in predicting absolute stability of...

Identifying patterns of selection at synonymous sites in a Pseudomonas phylogeny.

A growing body of evidence suggests that synonymous substitutions, DNA sequence changes that do not alter the encoded amino acid and so should be selectively neutral, can be under strong selection. Yet our ability to identify putative non-neutral synonymous substitutions from comparative sequence data is limited. Here,...

Targeting Mcl-1 to Restore IL-10-Driven Breg Suppression Reverses Allergic Asthma.

BACKGROUND Regulatory B cells (Bregs) suppress allergic inflammation primarily through interleukin-10 (IL-10), yet the intrinsic mechanisms constraining their regulatory capacity remain incompletely understood. Although the anti-apoptotic protein Mcl-1 is essential for B cell survival, its potential non-canonical roles...

Poly(I:C) stimulation upregulates HLA-G expression in human nasal epithelial cells.

Human leukocyte antigen (HLA)-G is an immunosuppressive molecule involved in inflammation and has been reported to be induced by viral infections. Although the upper airway is a major entry site for viral pathogens, the expression of HLA-G in the nasal mucosa and its regulatory mechanisms remain unclear. We investigate...

Orthogonal Decoupling of First- and Second-Shell Contributions in Protein-Supported Single-Atom Catalysis.

Single-atom catalysis is predominantly interpreted through the electronic structure of the metal center and its first coordination sphere, whereas the independent contribution of the second shell remains difficult to isolate experimentally. Here, we report a protein-supported single-atom catalytic platform that enables...