Identification of novel paralytic shellfish toxin binding protein via homology modeling and molecular docking

Abstract

A paralytic shellfish toxin binding protein (PST-BP) was extracted and purified from the viscera of oyster (Crassostrea hongkongensis) that accumulates paralytic shellfish toxin (PST), and the amino acid sequence of the protein was detected via HPLC-MS-MS. The structure of the PST-BP was built by homology modeling, and the interaction between PST and PST-BP was studied using molecular docking. The results showed that the purity of PST-BP was more than 99.8% after the purification. The PST-BP carried a molecular weight of 33.5 kDa and sequence alignment revealed its high sequence similarities with glyceraldehyde-3-phosphate-dehydrogenase (GAPDH). It has been shown that 99.9% of the amino acid residues in the PST-BP homology model are within a reasonable range, which exceeds the 90% threshold requirement for residuals in high-quality model structures. The molecular docking results revealed that Arg, Asp, Lys, Ala, Ser, Gln, Gly, Trp, Asn, Met, and Pro were identified as the major interacting amino acids residues between PST-BP and PST.

Keywords: Gonyautoxins; Homology modeling; Molecular docking; Paralytic shellfish toxin-binding protein.