Self-assembly of a Peptide [2]Catenane through Ω-Loop Folding

Abstract

In this work, a peptide [2]catenane was created by exploiting the strong tendency of the Pro-Gly-Pro (PGP) sequence to fold into an ³-loop. Ditopic heptapeptide ligand 1, which includes the PGP sequence, formed peptide [2]catenane 2 on complexation with Ag + . Moreover, addition/removal of Na + triggered a reversible structural change between 2 and twisted macrocycle 3. Keywords: Interlocking molecules | Peptide folding | Structural switchPeptide loops are inconspicuous but important structural elements of proteins and can induce strand entanglement, as often seen in protein knots and catenanes.1 Such entanglements are believed to enhance the mechanical stability of proteins. Unlike the artificial design of α-helix/β-sheet mimics, 2 that of peptide-loop conformations remains difficult because of the absence of intra-strand hydrogen bonds in the loop, and it is therefore largely unexplored. Recently, we reported that the short Pro-Gly-Pro (PGP) peptide sequence is folded into an "³"-shaped loop on concerted metal-coordination, and this gives rise to a highly entangled 12-crossing [4]catenane.3 In this selfassembly, the latent ³-folding propensity of the PGP sequence is expressed by inter-strand interactions during the entanglement of the two loop motifs. To generalize this observation and demonstrate the potential of the folding-and-assembly strategy for creating highly complex discrete structures, we designed new ditopic heptapeptide ligand 1, in which PGP and GPP tripeptide sequences are linked through a rigid imino(1,3-phenylene)carbonyl spacer (Scheme 1). We show that, through Ag + -triggered folding and assembly, ligand 1, which has a longer and more flexible peptide sequence than the ligand used in our previous study, was folded into an expanded ³-loop and assembled in concert into peptide [2]catenane 2 ([(Ag¢1) 2 ] 2+ ). This catenane structure appears to be stabilized by various inter-strand interactions between the two peptide macrocycles (hydrogen bonding, ππ, Agπ). Upon addition of Na + , the inter-strand hydrogen bonding was disrupted by the Na + £O=C coordination and 2 unexpectedly underwent a drastic structural change into a [Ag 2 (1) 2 Na] 3+ macrocycle. Thus, a flexible loop can also serve as a building block for dynamic peptide-based assemblies.Pyridine-tethered heptapeptide 1 was synthesized by solution-phase peptide synthesis (see the Supporting Information (SI)). Complexation of 1 with Ag + was first carried out using a crystallization strategy. Triple layers of peptide ligand 1 (5¯mol) in CHCl 3 (0.15 mL), a buffer solution (0.15 mL, CHCl 3 /EtOH = 1:1 (v/v)), and silver(I) bis(trifluoromethylsulfonyl)imide (AgNTf 2 , 5¯mol) in EtOH (0.15 mL) were prepared in a capped microtube and slowly diffused into each other at 10°C. After a few days, single block-shaped crystals of excellent quality were obtained. A crystallographic study revealed the formation of [2]catenane 2, in which the two [Ag¢1]+ macrocycles are interlocked in C 2 symmetry (Figure 1a). The interlocked structure is induced by mult...

A metal–peptide capsule by multiple ring threading

“…39). This is also observed in previous [2]catenane 2 4 . The crossing number of this topology is 24 (2 × 12 edges), and this was clearly confirmed by the reduced alternating link diagram 9 shown in Fig.…”

“…Six of these macrocycles form a cubic assembly through ring threading at each peptide hairpin; this corresponds to the T 2 -hexahedral link. Although the linking of two directional (chiral) macrocycles can generate diastereomers in principle, the 1 H NMR observation of the single product indicates the threading process takes place with complete diastereo-selectivity here as observed in the previous study on 2 4 . Each vertex (three-way junction structure) of this topology is induced by six sets of inter-strand amide hydrogen bonds (Fig.…”

“…Previously, the self-assembly of Ag + and ditopic oligopeptide 1 has resulted in peptide [2]catenane 2 (Fig. 1a) 4 . The Pro-Gly-Pro-x-Gly-Pro-Pro sequence (Pro: l -proline, Gly: glycine, and x: imino-(1,3-phenylene)carbonyl spacer) of 1 adopted a loop conformation on coordination to Ag + and assembled to form a simple link of two Ag 1 ( 1 ) 1 macrocycles.…”

Metal–peptide rings form highly entangled topologically inequivalent frameworks with the same ring- and crossing-numbers

“…11a, b). The highly dispersed aromatic and amide proton signals observed between 6.9 and 10.7 ppm are indicative of the formation of a highly entangled structure and have previously been observed in peptide-based catenanes 16,20 . Diffusion-ordered spectroscopy (DOSY) measurements also support the formation of a single product (Supplementary Fig.…”

“…There are great advantages to the rapidly developing DNA nanotechnology method 22,23 , which can be used to manipulate a variety of advanced entangled nanostructures, but this method also has disadvantages, including its poor efficiency in three-dimensional shape construction, structural modification, and large-scale synthesis. However, these problems can be addressed by our folding-and-assembly method 16,20,24–26 if the structural prediction is accompanied hereafter. Considering the abundance of highly entangled nanostructures in biological systems and their contribution to the formation and stabilisation of giant protein assemblies 27–30 , molecular entanglements can be considered a new nanoscale bonding pattern representing the principles of nature.…”