Principal Component and Structural Element Analysis Provide Insights into the Evolutionary Divergence of Conotoxins

SIMPLE SUMMARY: Conotoxins are small, structured components found in the venom of predatory cone snails. They were proven to be valuable probes and models for drug discovery and protein evolution studies. Conotoxins present an opportunity to study protein divergence and discover potential human therapeutic landscapes. Although there is considerable literature on conotoxin evolution and activity, what pushed conotoxin divergence remains unclear. Hence, in this paper, we conducted a two-phase study that investigated conotoxin evolution in terms of divergence, followed by structural analysis to determine the relevant structural elements. By understanding the evolution of conotoxins, we identified patterns that account for their superior specificity. The results revealed similarities based on the cone snail’s diet preference. The structural elements are in synch with their target prey preference as if cone snails evolved to fine-tune their conopeptide armory to respond to evolutionary pressures by producing conotoxins selective for their prey of choice. We identified several structural elements that account for this specificity. Conservation patterns are observed within diet subgroups but are divergent from other groups. ABSTRACT: Predatory cone snails (Conus) developed a sophisticated neuropharmacological mechanism to capture prey, escape against other predators, and deter competitors. Their venom’s remarkable specificity for various ion channels and receptors is an evolutionary feat attributable to the venom’s variety of peptide components (conotoxins). However, what caused conotoxin divergence remains unclear and may be related to the role of prey shift. Principal component analysis revealed clustering events within diet subgroups indicating peptide sequence similarity patterns based on the prey they subdue. Molecular analyses using multiple sequence alignment and structural element analysis were conducted to observe the events at the molecular level that caused the subgrouping. Three distinct subgroups were identified. Results showed homologous regions and conserved residues within diet subgroups but divergent between other groups. We specified that these structural elements caused subgrouping in alpha conotoxins that may play a role in function specificity. In each diet subgroup, amino acid character, length of intervening amino acids between cysteine residues, and polypeptide length influenced subgrouping. This study provides molecular insights into the role of prey shift, specifically diet preference, in conotoxin divergence.