On the Design of Zinc‐Finger Models with Cyclic Peptides Bearing a Linear Tail

Abstract

Cyclic peptides with a linear tail (CPLT) have been successfully used to model two zinc fingers (ZFs) adopting the treble-clef- and loosened zinc-ribbon folds. In this article, we examine the factors that may influence the design of such ZF models: mutations in the sequence, size of the cycle, and size of the tail. For this purpose, several peptides derived from the CPLT-based models of the treble-clef- and loosened zinc-ribbon ZF were synthesized and studied. CPLT-based models appear to be robust toward mutations, accommodate various cycle sizes, and are sensible to the size of the linking region of the tail located between the cycle and the coordinating amino acids. Based on these criteria, we describe the design of a new CPLT-based model for the zinc-ribbon ZFs, LZR , and compare it to a linear analogue, LZR(lin) . The model complex Zn⋅LZR is able to fold correctly around the metal ion contrary to Zn⋅LZR(lin) , suggesting that CPLT-based models are more likely to yield structurally meaningful models of ZF sites than linear peptide models. Finally, we draw some rules that could allow the design of new CPLT-based metallopeptides with a controlled fold.

Model peptide for anti-sigma factor domain HHCC zinc fingers: high reactivity toward 1O2 leads to domain unfolding

“…Zn·L ASD (HHCC). The intensity of this band is Δ ε = 6600 M –1 cm –1 , which is in agreement with two zinc-bound cysteinates 20,24,29. To gain further insight into the coordination sphere of the Zn 2+ ion, L ASD (HHCC) was titrated with Co 2+ , a Zn 2+ ion surrogate commonly used to probe its geometry and coordination sphere.…”

“…For several years, we have been developing peptidic zinc finger models of small size in order to study the reactivity of zinc finger sites toward reactive oxygen species such as H 2 O 2 ,18–20 HOCl34 or 1 O 2 21,22 at the molecular level. Our approach involves the use of cyclic and branched peptides, named CPLT (Cyclic Peptides with Linear Tail),29 to create shortcuts in native zinc finger sequences. This affords models that reproduce almost perfectly the fold of native zinc finger domains around the Zn 2+ ion with a minimal set of amino acids.…”

Near diffusion-controlled reaction of a Zn(Cys)4 zinc finger with hypochlorous acid

“…We have described previously a model peptide for the zinc finger site of Hsp33. 34 This peptide, namely L HSP , is based on a cyclic peptide bearing a linear tail 35 and is designed to match the amino acid sequence and the structure of Hsp33 ( Fig. 1A ).…”

Efficient Oxidation and Destabilization of Zn(Cys)4 Zinc Fingers by Singlet Oxygen

“…We have developed a family of peptides modeling zinc fingers of various folds in order to study their reactivity with oxidants involved in oxidative stress 15–17. Concerning 1 O 2 , we decided to explore its reactivity with Zn⋅L TC , which models one of the most encountered ZF folds, the treble‐clef (Figure 1).…”