Disulfide Rearrangement Driven Changes in the Structure, Dynamics, and Conformational Stability of Conotoxin Pl14A

Abstract Conotoxin Pl14A, a 25-residue peptide from the venom of the cone snail Conus planorbis, contains four cysteines that can pair in three ways, yet only the globular connectivity (Cys7–Cys22, Cys11–Cys24) is found in nature. Using classical and replica-exchange molecular dynamics, we compared it with the ribbon (Cys7–Cys24, Cys11–Cys22) and bead (Cys7–Cys11, Cys22–Cys24) isomers. The globular isomer stays compact, retaining its helix and a persistent intramolecular hydrogen-bond network and coordinated motion, and occupies a single deep free-energy basin, whereas the ribbon isomer is partially disordered and has an unstable secondary structure, with a shallow landscape. The bead isomer, which has no disulfide linking the two halves of the peptide, rearranges early into a non-native structure with a new β-bridge and a fragmented landscape. Conformational stability therefore follows the order globular > ribbon > bead, and the intramolecular free energy favors the globular isomer over both alternatives, most strongly over the bead. Simulations of the reduced peptide show that this preference is already encoded in the sequence without disulfide bonds, the peptide mostly adopts a globular-like fold, and most of its bonding-competent cysteine geometries match the globular pairing. The disulfides thus reinforce, rather than dictate, a fold the sequence already favors, and pairings that conflict with it destabilize the peptide, most strongly when no long-range disulfide remains. These results help explain connectivity selection in conotoxins and other disulfide-rich peptides, with implications for peptide engineering.