Akademik Veri Yönetim Sistemi
VI. International Enzyme and Bioprocess Days, Kocaeli, Türkiye, 27 - 29 Ağustos 2025, ss.75, (Özet Bildiri)
Rab proteins are small GTPases that play essential roles in vesicle trafficking, organelle biogenesis, and membrane transport. Rab1A and Rab1B are particularly involved in protein transport from the endoplasmic reticulum to the Golgi apparatus. Proper function of these proteins is vital for cellular homeostasis, and their dysregulation has been linked to Parkinson’s disease, cancer, and inflammation, making them promising biomarkers and therapeutic targets.Zebrafish (Danio rerio) have emerged as a valuable model in cancer research due to their high genetic similarity to humans, rapid development, and transparent embryos. Approximately 82% of human disease-related genes have at least one ortholog in zebrafish, enhancing their relevance in translational studies.
In this study, the amino acid sequences of zebrafish Rab1A and Rab1B were retrieved from the UniProt database. Physicochemical properties were analyzed using ProtParam. Homology models were generated using MODELLER and validated with PROCHECK, Verify3D, and Ramachandran plot analyses. Molecular docking was performed with AutoDock Vina to assess ligand binding, followed by 50 ns molecular dynamics (MD) simulations using GROMACS to evaluate structural stability and dynamics. Secondary structure analysis showed comparable α-helix and β-sheet content for both proteins. GDP/GTP substrates exhibited strong binding affinity to Rab1A and Rab1B. MD simulations confirmed the overall stability of the protein-ligand complexes and demonstrated conformational changes upon ligand binding. Minor but significant differences in ligand-binding regions suggested functional divergence between Rab1A and Rab1B. These findings contribute to the understanding of Rab1 proteins as potential therapeutic targets and support their use in zebrafish-based translational research models.