Biology subjects

Cron, L.

Publications and source records attributed to Cron, L..

2 recordsLinked to original sources

bioRxiv2026

Structural analyses of Trichomonas vaginalis pyrophosphate-dependent phosphofructokinase (TvPPi-PFK)

Trichomonas vaginalis causes trichomoniasis, the most common non-viral sexually transmitted disease in humans. T. vaginalis pyrophosphate-dependent phosphofructokinase (TvPPi-PFK) is a putative target for rational, structure-based drug discovery, given its absence in mammals and its importance for parasite survival. TvPPi-PFK is a cytosolic enzyme that catalyzes the phosphorylation of fructose-6-phosphate using pyrophosphate (PPi) as the phosphoryl donor. This reversible reaction, catalyzed by TvPPi-PFK, is the first committed step in glycolysis. Its reverse reaction is vital for gluconeogenesis in T. vaginalis. The purification, crystallization, structure determination, and crystal structures of TvPPi-PFK are reported. TvPPi-PFK is the first reported eukaryotic PPi-PFK structure. TvPPi-PFK retains the overall PPi-PFK topology observed in bacterial PPi-PFK including conserved motifs essential for pyrophosphate binding and PPi-PFK catalytic activity. In addition to the catalytic PPi-PFK binding sites, TvPPi-PFK has two additional ligand binding sites. The first binds AMP usurped during protein production and helps stabilize the TvPPi-PFK tetramer. A second ligand binding site was observed in proximity to the AMP-binding site and accommodates sugar phosphates soaked into preformed crystals. This sugar phosphates binding site is distinct from the TvPPi-PFK active site that binds fructose-6-phosphate. Future mutagenesis and activity studies are planned to determine the relevance of both sites. SynopsisThe production, crystallization, and crystal structures of a pyrophosphate-dependent phosphofructokinase from Trichomonas vaginalis (TvPPi-PFK) are reported. TvPPi-PFK has a prototypical PPi-PFK active site as well as unexpected AMP and sugar-phosphate binding sites at the dimer interface.

biochemistry↗

bioRxiv2026

Automated extraction and optimization of protein purification protocols using multi-agent large language models

Recent advances in Large Language Models (LLMs) present new opportunities for automating critical bottlenecks in scientific workflows such as literature reviews or protocol design. One such bottleneck is the purification of recombinant proteins, a vital aspect of biomedical research that frequently fails. To improve success rates, researchers must manually define optimal large-scale purification conditions and establish robust rescue protocols for proteins with low stability or solubility - a time-intensive process. To address this gap, we introduce a multi-agent LLM system that automates the creation and optimization of protein purification protocols to facilitate the production of high-concentration, high-purity protein samples. Our application streamlines the labor-intensive manual process of sequence similarity searches, literature reviews, and protocol comparison. Operating in a tool-like constrained workflow, the system identifies analogous proteins, leverages specialized LLM agents to extract successful purification methodologies from primary source literature, and cross-references them against failed protocols to generate optimization recommendations. Evaluation on a select number of targets demonstrated high accuracy in protocol extraction and the generation of scientifically sound, expert-validated optimization recommendations. While this system reduces complex analysis time from hours to minutes, we identify the lack of programmatic open access to literature, specifically primary citations in the Protein Data Bank, as a fundamental limitation to LLM agent-based scientific workflows. Ultimately, this system demonstrates the feasibility of using LLM agents to streamline wet-lab workflows while preserving methodological transparency and reproducibility.

bioinformatics↗