Molecular dynamics simulations and free energy calculations of protein-peptide systems: binding mechanism of α-conotoxin SI to neuromuscular nicotinic acetylcholine receptor

Recently, morphine is the most used molecule for analgesia. However, morphine can be hazardous when it is used regularly because of its addictive nature. It can be obtained easily and its production cost is low. Because of this fact there is no other alternative to morphine. However there molecules with white hope are provided by the nature. Specifically, the toxins produced by venomous animals, are peptides which are able to be used for analgesia. Although investigation of the mechanisms and transforming into a drug of such peptides cost high amounts of money and time by using experimental techniques, the computer technology provides an opportunity to carry out such studies, currently. In this study, the interaction between α-Conotoxin peptide, which is an alternative to morphine, and neuromuscular nicotinic acetylcholine receptor has been investigated. Most probable bound configurations for these protein and ligand and their bounded dynamics has been investigated.