Characterization, protein modeling, and molecular docking of factor C from Indonesian horseshoe crab (Tachypleus gigas)

Background Horseshoe crab (Tachypleus gigas) amebocytes are useful biomedical components for endotoxin detec tion, and their growing needs for biomedical purposes cause the horseshoe crab population to decline. Factor C syn thesis via genetic engineering offers a solution to replace natural horseshoe crab’s factor C and prevent its excessive harvest from nature. In response to these concerns, this study aimed to characterize the amebocyte lysates and factor C protein modeling of T. gigas originated from Banyuasin South Sumatra Estuary. Methods and results Sampling of T. gigas was carried out in Banyuasin South Sumatra Estuary, Indonesia. The endo toxin test or TAL (Tachypleus amebocyte lysates) assay was performed using gel coagulation method. Protein charac terization of protease enzyme was conducted by protease activity, SDS-PAGE, and zymogram analysis. The cDNA of mitochondrial COI gene was amplified for molecular identification followed by cDNA cloning of factor C. Protein mod eling was investigated by molecular docking and molecular dynamic (MD) simulation. Endotoxin test results showed that TAL-35 had endotoxin sensitivity in a range of 0.0156–1 EU/ml, while TAL 36 had a sensitivity between 00,625 and 1 EU/ml. T. gigas amebocytes have protease activity in molecular mass sizes less than 60 kDa, with 367 U/ml for TAL 35 and 430 U/ml for TAL 36. The molecular identification revealed 98.68% identity similarity to T. gigas. The docking results suggested three ligands; i.e., diphosphoryl lipid A, core lipid A, and Kdo2 lipid A can be activators of the factor C protein by binding to the region of the receptor to form a ligand-receptor complex. Conclusions Endotoxins can be detected using horseshoe crab amebocytes. The presence of proteases is consid ered responsible for this ability, as evidenced by casein zymogram results. According to docking and MD analysis, we found that lipopolysaccharides (LPS) participate to the binding site of factor C. Keywords Amebocyte lysate, Endotoxin, Factor C, Tachypleus gigas, Molecular dynamic