PS-ODNs have a PS backbone, and PO-ODNs have a native PO backbone.
A fundamental aspect that we revealed is the dynamic stabilization mechanism for the GPO repeat: gpo10 has low-occupancy, short-lived native backbone H-bonds, which is an effective strategy to maintain the triple helical structure while remaining flexible.
The unfolding process of the peptide occurs in two steps because of the accumulation of a metastable on-pathway intermediate state stabilized by two native backbone hydrogen bonds assisted by nonnative hydrophobic interactions between the tryptophan side chains.
The high stiffness of the imino-rich domain N-terminal to the cleavage site is a result of unwinding without separation of α chains that appears to promote native backbone H-bond formation.
Indeed, the refinement protocol is able to sample a near-native conformation in only 10 of the 26 interactions (compared to 25/26 for theFlexPepDock ab-initio protocol described here; Fig. 2A), and these 10 are the easier cases where the native backbone conformation is already extended-like.
To address this, we compared the predicted side-chain structures given the native backbone structures and those given the predicted backbone structures in terms of free energy.
Several side-chain prediction tools have been proven to predict accurate side-chain structures from native backbone structures [ 8, 9, 25, 26].
The other native backbone hydrogen bonds (i.e., in distal or proximal position) may or may not be present, indicating that their formation is not rate-limiting.
The correspondence of the fluorescence kinetics with the slowest IR phase indicates that burial of the Trp is concomitant with the folding to the native backbone topology.
Loss of native backbone H-bonds and increase in Rg dominates the second and third principal components under 500 K and 600 K.
