Induction and destruction of folding motifs in cyclotides by cyclic cystine knots

Abstract

Multivariate roles of cyclic cystine knots (CCK) present in cyclotides are well known. More than often this marvellous combination of disulphide linkages embedded in a macrocyclic backbone is seen to induce and stabilize otherwise unfavourable secondary structural motifs in peptides. Partial or complete reduction of the disulphide bonds leads to significant overhauling of the peptide structure and associated dynamics with disappearance of some of the CCK-stabilized local motifs. In this work, we explore structural and dynamical intricacies in two prototypical bracelet and a Möbius cyclotide, respectively cycloviolacin O1 (cyO1), cycloviolacin O2 (cyO2) and kalata B1 (kB1), either in their native (N, with CCK), partially reduced (with either one or two S-S bonds) or completely reduced (D, without CCK) forms using molecular dynamics simulations. The S-S linkage(s) primarily responsible for sustaining a given organized motif in each case is identified from the simulation of the partially reduced forms. Correlation of helix propensity, strand propensity and hydropathicity indices of the amino acids conserved across families of different bracelet/Möbius cyclotides give insight to the natural inclination of the CCK stabilized backbones to exhibit a given motif. Dihedral principal component analysis (dPCA) and normal mode analysis (NMA) help scan through the effect of structural reorganization on peptide dynamics. The relatively restricted dynamical modes in CCK-intact native peptides are replaced with large amplitude dynamical fluctuations in the reduced peptides. Concomitant structural variance is observed across the clusters in the space spanned by the dominant principal components (PCs).