Elucidating structural determinants in the functional regions of toxins can provide useful knowledge for designing novel analgesic peptides. Glycine residues at the C-terminal region of the neurotoxin BmK AGP-SYPU2 from the scorpion Buthus martensii Karsch (BmK) have been shown to be crucial to its analgesic activity. However, there has been no research on the structure-function relationship between the C-terminal segment of this toxin and its analgesic activity. To address this issue, we performed three MD simulations: one on the native structure and the other two on mutants of that structure. Results of these calculations suggest that the existence of glycine residues at the C-terminal segment stabilizes the protruding topology of the NC domain, which is considered an important determinant of the analgesic activity of BmK AGP-SYPU2.