δ-Conotoxin Structure Prediction and Analysis through Large-Scale Comparative and Deep Learning Modeling Approaches

The δ-conotoxins, a class of peptides produced in the venom of cone snails, are of interest due to their ability to inhibit the inactivation of voltage-gated sodium channels causing paralysis and other neurological responses, but difficulties in their isolation and synthesis have made structural characterization challenging. Taking advantage of recent breakthroughs in computational algorithms for structure prediction that have made modeling especially useful when experimental data is sparse, this work uses both the deep-learning-based algorithm AlphaFold and comparative modeling method RosettaCM to model and analyze 18 previously uncharacterized δ-conotoxins derived from piscivorous, vermivorous, and molluscivorous cone snails. The models provide useful insights into the structural aspects of these peptides and suggest features likely to be significant in influencing their binding and different pharmacological activities against their targets, with implications for drug development. Additionally, the described protocol provides a roadmap for the modeling of similar disulfide-rich peptides by these complementary methods.