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Chow, C. F. W.

Publications and source records attributed to Chow, C. F. W..

3 recordsLinked to original sources

Born to Condense: Polysomes Drive Co-Translational Condensation of Biomolecular Condensate Proteins

Biomolecular condensates formed by protein liquid-liquid phase separation (LLPS) are ubiquitous in cells and play crucial roles in cellular regulation. While the physics and functions of LLPS are well studied, its interplay with protein synthesis - translation - remains largely unexplored. Here we introduce a theoretical framework for Co-Translational Condensation (CTC), in which nascent protein chains of polysomes - multiple ribosomes on one mRNA - interact with condensates, localizing translation to condensate surfaces. Using coarse-grained simulations, we show that protein domain architecture dictates the thermodynamics of CTC, consistent with a Langmuir adsorption model. Bioinformatic analysis of more than 7,500 proteins reveals that most condensate-associated proteins have architectures favoring CTC, with strong interaction regions of nascent chains exposed on polysomes. At the dynamical level, simulation and reaction-diffusion modeling reveal that CTC is kinetically feasible within typical polysome lifetimes, either through large polysomes nucleating new condensates or via diffusion to pre-existing condensates. As a case study, we demonstrate that CTC enhances post-translational modifications by minimizing unmodified intermediates. More broadly, we anticipate CTC may also influence protein folding, misfolding, and signal-integration latency. Together, our results establish CTC as a general mechanism coupling translation with phase separation, with broad implications for protein evolution, cellular organization, and synthetic biology.

biophysics↗

SHARK enables homology assessment in unalignable anddisordered sequences

Intrinsically disordered regions (IDRs) are structurally flexible protein segments with regulatory functions in multiple contexts, such as in the assembly of biomolecular condensates. Since IDRs undergo more rapid evolution than ordered regions, identifying homology of such poorly conserved regions remains challenging for state-of-the-art alignment-based methods that rely on position-specific conservation of residues. Thus, systematic functional annotation and evolutionary analysis of IDRs have been limited, despite comprising [~]21% of proteins. To accurately assess homology between unalignable sequences, we developed an alignment-free sequence comparison algorithm, SHARK (Similarity/Homology Assessment by Relating K-mers). We trained SHARK-dive, a machine learning homology classifier, which achieved superior performance to standard alignment in assessing homology in unalignable sequences, and correctly identified dissimilar IDRs capable of functional rescue in IDR-replacement experiments reported in the literature. SHARK-dive not only predicts functionally similar IDRs, but also identifies cryptic sequence properties and motifs that drive remote homology, thereby facilitating systematic analysis and functional annotation of the unalignable protein universe.

bioinformatics↗

Phenethylamine-producing gut bacteria induces diarrhea-predominant irritable bowel syndrome by increasing serotonin biosynthesis

Despite the strong association between gut microbial dysbiosis, serotonin (5-HT) dysregulation and diarrhea-predominant irritable bowel syndrome (IBS-D), the mechanism by which changes in the gut microbiota contribute to the pathogenesis of IBS-D, particularly the role of dysregulated 5-HT production, remains unclear. The present study identified Ruminococcus gnavus in the human gut microbiota as a key risk factor of IBS-D. R. gnavus was significantly enriched in IBS-D patients and exhibited positive correlation with serum 5- HT level and severity of diarrhea symptoms. We showed that R. gnavus induced diarrhea-like symptoms in mice by promoting microbial shunting of essential aromatic amino acids to aromatic trace amines including phenethylamine and tryptamine, thereby stimulating the biosynthesis of peripheral 5-HT, a potent stimulator for gastrointestinal transit. This study identify gut-microbial metabolism of dietary amino acids as a cause of IBS-D and lays a foundation for developing novel therapeutic target for the treatment of IBS-D. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/483096v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@48400aorg.highwire.dtl.DTLVardef@1645aedorg.highwire.dtl.DTLVardef@18d878dorg.highwire.dtl.DTLVardef@be4b30_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗