Impact of Point Mutation on Shiga-like Toxin 1: A Molecular Dynamics Simulation Study

Abstract

The causative agent of gastroenteritis is Shiga toxin, which belongs to a functionally and structurally associated protein family despite each individual having a unique amino acid sequence. After entering the ER lumen and relocating the toxic domain to the cytoplasm, they alter the large subunit of rRNA, preventing protein synthesis and ribosomal damage. Shiga-like toxin-1 (SLT-1) subunit B targets glycolipid receptor Gb3, which plays a significant role in cytotoxicity. Though the mutational effect on subunit B is important for cytotoxicity study, we lack better understanding. Our present study targets the mutational impact of glycine protein at their 62th amino acid sequence of subunit B. For example, how it can alter the receptor-binding capacity and virulence. We used in silico method with GROMACS software suite (version 5.2, 2020.1) on Google Colab for a 100ns (100,000ps) simulation period and UCSF Chimera software for visualizing mutant and wild-type structure similarities. Surprisingly, RMSD, RMSF, and Rg trajectories from the simulation analysis indicated a more stable and compact mutant structure than the wild type. Principle component analysis (PCA) and SASA were visualized for the entire 100ns, which pointed towards homogeneity between both structures and more solvent accessibility in the mutant structure. This mutation may elevate receptor-binding and virulence capacity. Moreover, this finding can offer a better insight for future vaccine production.