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Abstract The three dimensional organization of the genome plays a critical role in gene regulation and cellular function. Unlike folded globular proteins, chromosomes exhibit high structural variability and must be described as ensembles of dynamic conformations rather than as single stable states. This chapter explore...
A static magnetic field (SMF)-assisted liquid-state fermentation strategy using Lacticaseibacillus paracasei (L. paracasei) is proposed to improve the comprehensive utilization value of Ginkgo biloba leaves. Taking total flavonoid extraction yield as the objective, Box-Behnken response surface methodology was adopted t...
The extensive proteome remodeling in the (p)ppGpp-null relA spoT mutant during late exponential and stationary phase and the first protein-level analysis of the stringent response in P. aeruginosa are characterized, highlighting the role of (p)ppGpp in shutting down broad metabolic functions and activating adaptive pat...
Messenger RNA (mRNA) therapeutics have transformed vaccination and protein replacement strategies, yet efforts to improve their performance have focused largely on sequence engineering, nucleotide modification, and delivery vehicles. Here we show that mRNA function can be controlled by rational design of higher-order R...
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Theoretical and Computational Approaches to Nucleic Acid Folding, Interaction, and Assembly. The energy landscape framework offers a powerful lens for understanding how DNA and RNA fold, interact, and assemble. Readers will encounter theoretical and computational approaches for mapping these landscapes encompassing the...
J-domain proteins (JDPs) direct Hsp70 functions through a conserved J-domain that engages and activates Hsp70. JDPs support proteostasis and are linked to development and disease, yet how they are regulated remains unclear. Here, we identify a conserved tyrosine motif outside the canonical four-helix J-domain core, as...
Abstract RNA can exhibit a broad range of properties that impact biological processes such as signaling and gene expression. A characteristic feature of RNA is its high negative charge, which arises from the phosphodiester backbone. To overcome the repulsive nature of backbone-backbone interactions during folding, RNA...
Findings identify glutamine-regulated VCP acetylation as a metabolic–proteostasis dependency in RB1-deficient tumors and nominate VCP inhibition as a therapeutic strategy for this difficult-to-target tumor state.
Plant molecular farming has emerged as a promising platform to produce recombinant biopharmaceuticals. The expression of foreign proteins changes the host proteome and metabolome, and these changes might have an effect on the accumulation of recombinant proteins. In this study, we investigated how fusion partners and E...
Cordyceps militaris polysaccharides exhibit significant in vitro anticoagulant activity, acting through potential multi-pathway mechanisms and pronounced fibrinogen reduction, and their potential development as functional food ingredients or biomedical agents for the prevention of thrombotic cardiovascular and cerebrov...
The two paralogs YAP and TAZ act through TEAD transcription factors and bind PPxY motif proteins in the Hippo pathway via WW domains. YAP has up to two WW domains, whereas TAZ has one. Because YAPWW1 and TAZWW are the most similar in sequence, they can be considered as corresponding modules in these two proteins. This...
Tryptophan (Trp) residues are comparatively rare in proteins but are frequently positioned at sites that control folding, molecular recognition, ligand binding, and enzymatic activity. Direct chemical modification of Trp therefore offers a powerful strategy for perturbing protein structure and function. However, method...
Proof of concept for watermarking AI-generated proteins while preserving biological function.
A new machine-learning framework aims to improve the success rate of computational protein design while moving away from results that reproduce sequences found in nature.
Scientists are using AlphaFold to strengthen a photosynthesis enzyme for resilient, heat-tolerant crops.
Explore how AlphaFold has accelerated science and fueled a global wave of biological discovery.
AlphaFold has revealed the structure of a key protein behind heart disease
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