protein folding

Supplemental Material for: High-sensitivity C-Reactive Protein as a Risk-Enhancing Biomarker in Patients with Chronic Kidney Disease and Atherosclerotic Cardiovascular Disease: A Narrative Review

Background: Patients with chronic kidney disease (CKD) have a >10-fold higher risk of cardiovascular mortality than the general population, influenced by both traditional and non-traditional risk factors. Residual cardiovascular risk persists despite effective lipid lowering and antihypertensive treatment, suggesting t...

FAP-Triggered In Situ Self-Assembly of HPQ in Tumors Empowers 131I Internal Radiotherapy

Abstract Fibroblast activating protein (FAP) is specifically overexpressed in malignant tumors. The 2-(2′-hydroxyphenyl)-4(3H)-quinazolinone (HPQ) scaffold exhibits hydrophobicity, aggregation-induced emission (AIE). The responsive probes built on HPQ can undergo in situ activation and self-assembling precipitation, en...

Analysis of Ligation Activity in Miniaturized L1 Ligase Ribozyme Variants Down to 49 nt and in Split Ribozyme Forms

Identifying the smallest active unit capable of ligating RNA in the absence of proteins is important to elucidate ribozyme evolution. Here, we aimed to construct an evolutionary model of the L1 ligase ribozyme. The miniaturized L1 ligase ribozyme (L1X6c2) consists of three stems: Stems A, B, and C. Mutants with shorten...

BIMS-GA: Adaptive Multi-Objective Optimization for Network-Aware Pancreatic Ductal Adenocarcinoma Biomarker Discovery

Pancreatic ductal adenocarcinoma (PDAC) has a five-year relative survival of 8%. Feature selection optimizes accuracy, survival concordance, and network structure separately; whether uniting them matters has not been determined. The BIMS-GA optimizes the cross-validated AUC, Cox concordance, and STRING v11.0 protein–pr...

Introduction: Insertion and Folding of Membrane Proteins and Peptides

Reciprocal modulation between beef protein and wine phenolics during in vitro co-digestion: a proposed ternary complex-mediated mechanism modulated by cooking technique

Background Beef and red wine form a classic dietary combination, yet how their components reciprocally influence each other during digestion remains unclear. Methods This study co-digested steamed, boiled and grilled beef with red wine using the INFOGEST 2.0 in vitro digestion model, combined with molecular docking, to...

LNP Delivery of Prime Editors Enables Durable Correction of PAH R408W in Phenylketonuria Models

Phenylketonuria (PKU) is a monogenic metabolic disorder caused by mutations in the phenylalanine hydroxylase (PAH) gene, the most common of which is c.1222C>T (p.R408W). Current treatment options, including dietary restriction and enzyme substitution, can be effective but are often challenging for patients to maintain...

Peptide-based inhibitors of tau aggregation as a potential therapeutic for Alzheimer's disease

Tauopathies are a group of neurodegenerative diseases characterized by the deposition of misfolded and aggregated Tau protein in patients’ brains. Alzheimer's disease (AD), the most common tauopathy and leading cause of dementia, affects over 55 million people worldwide, with prevalence projected to double every two ye...

A self-adaptive tube restraint for free-energy calculations along path collective variables

Path collective variables (PCVs) reduce a high-dimensional transition to a progress coordinate, s, and an orthogonal distance, z. Computing the free energy along s often requires restraining z, so that sampling embraces a tube centered on the reference path. However, a conventional fixed half-harmonic wall demands an a...

Functional Properties and In Vitro Digestibility of an Underutilized Legume Ingredient: Drying-Induced Changes in Leucaena esculenta Flour

Abstract Leucaena esculenta is an underutilized legume traditionally consumed in Mexico with potential as a sustainable food ingredient. This study evaluated the effects of two traditional drying methods, sun drying (SUF) and shade drying (SHF), on the nutritional composition, color, antioxidant properties, mimosine co...

Diagnostic cancellation and benchmark mismatch in SOD1 folding free energy calculations

Alchemical free-energy calculations are increasingly used to predict how missense mutations change protein folding stability, and their reliability is usually judged by aggregate convergence diagnostics and agreement with experimental controls. This working paper reports a validation campaign for the apo, disulfide-red...

Single-Molecule Studies Reveal That Water Starts to Protect Proteins Even at the ppm Level

Abstract A consensus established by extensive thermodynamic and structural studies of proteins and DNA is that water acts as an indispensable structural cofactor rather than a passive solvent for biomolecules. Nevertheless, it remains unclear whether trace water still exerts a stabilizing effect on proteins under ultra...