Relationship between the structure and the enzymatic activity of crotoxin complex and its phospholipase A2 subunit: An in silico approach

Crotoxin, one of the major toxins of South American rattlesnake Crotalus durissus subspecies, is an heterodimeric complex composed of two distinct subunits: a basic phospholipase A2 (PLA2, CB) and an acidic nontoxic catalytically inactive protein, crotapotin (CA). It's well known that CB has a high enzymatic activity; however the molecular aspects that determine this fact remain unknown. In this study, an in silico approach was used to predict the CA structure by homology modeling, and the crotoxin structure by means of molecular docking. CA structure was built using the software Modeller taking Crotalus atrox PLA2 (1PP2:R) as a template. Different criteria measured by Procheck, Verify 3D and ProSA were indicative of the reliability and the proper fold for the predicted structural model of CA. Then, a combination of this model and CB crystal structure was used to build the structure of crotoxin complex through rigid-body protein–protein docking. The crotoxin-3D model suggested that by means of hydrophobic and π–π stacking interactions, CA-Y24 and CA-F119 interact with CB-F24 and CB-F119, respectively. Those interactions could prevent the interfacial adsorption of the CB onto the lipid/water interface by blocking part of the interfacial binding surface of the PLA2. This fact could explain the differences regarding to enzymatic activity between the crotoxin complex and CB. In addition, the crotoxin-3D model showed solvent-exposed regions of CA that could bind the receptor expressed in target cells.

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► An in silico approach was used to predict the CA structure by homology modeling.
► The 3D-structure of crotoxin complex was modeled by means of molecular docking.
► Hydrophobic and π–π stacking interactions were observed in crotoxin model.
► These interactions would block part of the interfacial binding surface of the PLA2.