Using yeast two-hybrid system and molecular dynamics simulation to detect venom protein-protein interactions

Proteins and peptides are major components of snake venom. Venom protein transcriptomes and proteomes of many snake species have been reported; however, snake venom complexity (i.e., the venom protein-protein interactions, PPIs) remains largely unknown. To detect the venom protein interactions, we used the most common snake venom component, phospholipase A(2)s (PLA(2)s) as a “bait” to identify the interactions between PLA(2)s and 14 of the most common proteins in Western diamondback rattlesnake (Crotalus atrox) venom by using yeast two-hybrid (Y2H) analysis, a technique used to detect PPIs. As a result, we identified PLA(2)s interacting with themselves, and lysing-49 PLA(2) (Lys49 PLA(2)) interacting with venom cysteine-rich secretory protein (CRISP). To reveal the complex structure of Lys49 PLA(2)-CRISP interaction at the structural level, we first built the three-dimensional (3D) structures of Lys49 PLA(2) and CRISP by a widely used computational program-MODELLER. The binding modes of Lys49 PLA(2)-CRISP interaction were then predicted through three different docking programs including ClusPro, ZDOCK and HADDOCK. Furthermore, the most likely complex structure of Lys49 PLA(2)-CRISP was inferred by molecular dynamic (MD) simulations with GROMACS software. The techniques used and results obtained from this study strengthen the understanding of snake venom protein interactions and pave the way for the study of animal venom complexity.