protein folding

Joint steering of protein generation across multiple target properties

Ideally, protein design could optimize several properties at once while ensuring the protein satisfies basic biophysical constraints such as folding, stability, solubility, and expression. However, most guided generation methods optimize only one or two simple objectives. We developed a workflow that uses predictive mo...

Transcriptomic Responses and Putative Mechanisms of Nicotinamide-Mediated Saline–Alkaline Tolerance in Soybean

This study systematically investigates the regulatory effect of exogenous nicotinamide on soybean saline–alkaline tolerance and identifies its candidate genes and putative mechanisms under salt-stressed conditions.

Uterine fluid proteomic and metabolomic profiles associated with soft-shelled egg formation in laying hens

Introduction Soft-shelled eggs are a major eggshell defect in poultry production, yet the underlying mechanisms of their formation remain unclear. The objective of this study was to characterize biological changes associated with soft-shelled egg formation in laying hens by integrating quantitative proteomics and untar...

Improving Yield and Assessing Quality of Secreted Proteins Over-Expressed in Pichia Pastoris with Chaperones and Structural Mass Spectrometry

It is demonstrated that maximizing recombinant protein production requires optimization of both yield and structural quality and establish complementary strategies for improving secreted protein expression in Pichia.

基于动态拓扑的生物分子动力学模拟

This paper presents a novel approach to biological molecular dynamics simulations utilizing dynamic topology. Traditional methods often rely on static molecular arrangements, limiting the ability to capture intricate interactions. We introduce a dynamic topology framework that dynamically adjusts the geometry of molecu...

Massively parallel characterization of RNA G-quadruplex stability and molecular recognition

RNA G-quadruplexes (rG4s) have been implicated as important regulators of RNA metabolism and are promising targets for RNA-targeted therapeutics. rG4s typically require a canonical (G≥2N1-7)4 motif, but the sequence features that affect rG4 stability and recognition by RNA-binding proteins (RBPs) and rG4-binding ligand...

Targeting PI3K decreases trogocytosis-mediated CAR T cell fratricide

CAR T cell-mediated trogocytosis (CMT) is a proposed mechanism of tumor immune evasion, in which the cognate interaction between CAR T cells and tumor cells results in the transfer of target antigen from the tumor cell surface to the CAR T cell. In addition to the emergence of antigen-negative target cells, antigen-pos...

Viscoelasticity and Interface Properties of Multi-Component Condensates Govern Protein Sequestration and Suppression of Amyloid Formation

CatESO: Differentiable Enzyme Sequence Optimization Guided by Substrate-Aware K cat Prediction

Abstract Enzymes drive biological chemistry and offer greener routes to chemicals, materials, and medicines, yet their broader use as biocatalysts is often limited by insufficient catalytic turnover. Improving turnover is hard: measured rate constants are scarce and protein sequence space is vast. Deep learning models...

基于动态拓扑的生物分子动力学模拟

This paper presents a novel approach to biological molecular dynamics simulations utilizing dynamic topology. Traditional methods often rely on static molecular arrangements, limiting the ability to capture intricate interactions. We introduce a dynamic topology framework that dynamically adjusts the geometry of molecu...

Title: Statistical Topology of Complex Structures

This paper investigates the statistical topology of complex structures, focusing on the identification of underlying patterns and prediction of emergent behavior within datasets exhibiting inherent statistical properties. We propose a novel method, the "Resonance Field" concept, to quantify these properties and establi...

Figure S2

Figure S2. Renal expression profile of qPCR-assessed candidate miRNA target genes in CLP and sham piglets. The horizontal bar plot shows log2 fold changes in renal mRNA expression in CLP relative to sham kidneys after normalization to 18S rRNA. Positive and negative values indicate higher and lower expression in the CL...