A High‐Resolution Structure that Provides Insight into Coiled‐Coil Thiodepsipeptide Dynamic Chemistry

Abstract

Stable and reactive: A crystal structure at 1.35 Å of a thioester coiled-coil protein reveals high similarity to all-peptide-bond proteins. In these assemblies, the thioester bonds are kept reactive towards thiol molecules in the mixture. This enables efficient domain exchange between proteins in response to changes in folding conditions or introduction of external templates.

A Bistable Switch in Dynamic Thiodepsipeptide Folding and Template‐Directed Ligation

“…[4e,g] As was shown for other thioester peptides, [16] we have recently elucidated that the formation of aw ell-folded coiled-coil structure by R renders it stable against the attack of peptide or small-molecule thiols,t hus significantly slowing down its decomposition, relative to the decomposition of unfolded peptides or peptides that form less stable coiled coils. [15] This observation implies ad isparity in rates of formation/decomposition of R in the autocatalyzed and uncatalyzed reactions.B ased on earlier theoretical predictions that even traditional (mass-action) kinetics,w ith adisparity in conversion of just one or two substrates,already carries the capacity for bistability, [14] and that hysteresis is am arker for complex landscapes in protein folding, [17] we hypothesize that the reversible formation of R from E and N may follow different pathways leading to bistability.F igure 1 shows the equilibration kinetics ( Figure 1b) Thee quilibration experiments were then repeated with reaction mixtures containing different total concentrations, ranging at 25-150 mm ( Figure 2). In all cases,aclear bistability picture was obtained, revealing SS equilibration with two significantly distinct K app values,e ach of narrow distribution (see standard-deviation bars in Figure 2).…”

Amino acid modifications for conformationally constraining naturally occurring and engineered peptide backbones: Insights from the Protein Data Bank

“…Another class of amino group modifications seen in the PDB includes isosteric replacement of N in the standard amino group with either sulphur or oxygen atoms forming thiodepsipeptides and depsipeptides, respectively . In a recent study, GCN4 coiled‐coil peptides (see also Section 3.2.1) were re‐engineered at Gly 18 with S‐modified Gly to form backbone thioester bonds (PDB ID 3w92) and O‐modified Gly to form backbone ester bond (PDB ID 3w93), respectively . Although the structure of these peptides are nearly identical to the engineered GCN4 coiled‐coil peptide with standard Gly18, the thiodepsipeptide derivative has showed more stability against hydrolysis and thiol‐dependent decomposition than its congeners …”

A Bistable Switch in Dynamic Thiodepsipeptide Folding and Template‐Directed Ligation

“…The bistable system was studied by following the reversible formation of a thioester peptide R from its precursor peptides, a shorter thioester, E , and a thiol‐terminated, N (Figure 1). Peptide R forms a trimeric coiled‐coil structure in neutral pH aqueous solutions (see Figure S1 in the Supporting Information),15 and can serve as a template for the association of E and N , enhancing their ligation by a thiol‐thioester exchange reaction 4e,g. As was shown for other thioester peptides,16 we have recently elucidated that the formation of a well‐folded coiled‐coil structure by R renders it stable against the attack of peptide or small‐molecule thiols, thus significantly slowing down its decomposition, relative to the decomposition of unfolded peptides or peptides that form less stable coiled coils 15.…”