388 papers
EnzySeek is an AI agent that leverages Large Language Models, a curated enzyme catalysis knowledge base, and Model Context Protocol interfaces to autonomously execute and validate complex enzyme simulation workflows—from protein structure prediction to QM/MM calculations—while continuously learning from human-verified results to advance the automation of enzyme catalysis research.
This study utilizes mass spectrometry-based profiling to reveal that women with polycystic ovary syndrome (PCOS) exhibit distinct serum bile acid dysregulation characterized by elevated levels of cholic and conjugated bile acids, which correlate with androgen levels and suggest a critical link between bile acid metabolism and the endocrine-metabolic dysfunction of PCOS.
This study introduces DONDI-5, a chemically stable solvatochromic fluorescent probe that mimics diacylglycerols, enabling live-cell visualization and providing direct experimental evidence that diacylglycerols can be transported to and transiently stored within lipid droplets without prior conversion to triacylglycerols.
This paper presents a nitro-reduction-based strategy that utilizes a redox-responsive carbamate modification to reversibly silence RNA function and enable its ultrafast, chemically controlled restoration, offering a versatile toolkit for temporal regulation of diverse RNA applications from CRISPR systems to living cells.
This study demonstrates that the bacterial ESCRT-III protein IM30 forms stress-responsive biomolecular condensates via liquid-liquid phase separation, a process driven by its structured 1-3 helical hairpin domain and triggered by environmental stress-induced acidification that lowers the phase-separation barrier.
This study elucidates the structural mechanism by which a nuclease-dead Cas12f protein, guided by RNA and complexed with a unique sigma factor, activates bacterial transcription by recruiting RNA polymerase to a specific downstream site while bypassing classical promoter recognition through novel stabilization of the melted DNA.
This study reveals that the deubiquitinating enzyme Otu1 (Yod1) prevents substrates from being trapped in futile cycles on the Cdc48/p97 ATPase by trimming their ubiquitin chains prior to translocation, thereby facilitating their efficient transfer to the proteasome for degradation through a conserved mechanism involving simultaneous cofactor binding and ubiquitin unfolding.
This study demonstrates that protein quantification and physical normalization steps can be omitted from certain quantitative proteomics workflows without significantly increasing measurement variability, provided that robust computational normalization strategies are applied during data analysis.
This study utilizes untargeted LC-MS metabolomics to identify distinct serum metabolic alterations in women with polycystic ovary syndrome, revealing disruptions in lipid, amino acid, and bile acid pathways that are significantly associated with insulin resistance and inflammation.
This study characterizes the phytochemical profile of the Vietnamese medicinal plant *Aruncus dioicus*, identifying eleven isolated compounds and demonstrating that specific phenylpropanoids, such as p-coumaric acid and cinnamic acid, exhibit potent in vitro antidiabetic activity by significantly inhibiting PTP1B and α-glucosidase enzymes.
This study reveals that pristine thermoplastic surfaces exhibit intrinsically low affinity for submicron carbon particles, *Escherichia coli*, and humic acid under low ionic strength conditions, where particle-specific properties dominate retention over collector characteristics and classical XDLVO theory fails to predict the observed weak attachment.
This study reveals that the bacterial enzyme FabB possesses a hidden secondary binding pocket that accommodates medium-to-long acyl chains in an alternate conformation, a structural feature absent in its homolog FabF that allows FabB to maintain catalytic function despite mutations that would otherwise disrupt substrate binding.
This study reveals that the arginine methyltransferases Hmt1 and PRMT1 promote the dissolution and clearance of α-synuclein aggregates under oxidative stress through a non-canonical, catalysis-independent mechanism, thereby reducing cellular toxicity and offering new therapeutic avenues for neurodegenerative diseases.
This study identifies ASCH domain-containing proteins across bacteria, archaea, and humans as a conserved family of tRNA N4-acetylcytidine (ac4C) deacetylases, revealing a widespread enzymatic mechanism for ac4C turnover beyond the previously known SIRT7.
This study determines the crystal structures of two new Hepatitis delta virus (HDV) ribozymes from *C. briggsae* and Ackermannviridae, revealing a conserved double-pseudoknot architecture and a catalytic mechanism where cytosine 75 acts as a general acid and a divalent metal ion functions as a Lewis acid, distinguishing this ribozyme class from most other nucleolytic ribozymes that rely on general base catalysis.
Using a peptidisc-enabled DIA-MS workflow, this study reveals that Alzheimer's disease in female APP mice causes significant cortical membrane proteome remodeling, which is selectively targeted by M1 receptor modulation to restore neuronal trafficking and synaptic plasticity pathways without broadly altering the wild-type membrane proteome.
This study identifies a critical SAP domain PIP motif within RAD18 that mediates its interaction with PCNA to drive mono-ubiquitination, establishing this structural interface as a key determinant of USP1-BRCA1 synthetic lethality and a potential mechanism of resistance to USP1-targeted therapies.
This study demonstrates that herring roe phospholipids promote the biosynthesis of specialized pro-resolving mediators (SPMs) in macrophages and psoriasis-relevant skin cell co-cultures, suggesting a mechanism by which these lipids facilitate the resolution of inflammation in psoriasis.
This paper describes the development and superior performance of a new-generation bifunctional lipid nanoparticle (mRNA-BLNP3) that utilizes dual-targeting glycolipids to selectively deliver mRNA to antigen-presenting cells, resulting in enhanced lymph node accumulation, reduced liver toxicity, and significantly improved humoral and cellular immune responses compared to previous generations.
This study utilizes deep redox proteomics to identify a druggable redox switch at Cys102 on the immune regulator SHP1, enabling the development of a selective covalent agonist that activates SHP1 to suppress macrophage inflammation.