β-Hairpins as peptidomimetics of human phosphoprotein-binding domains

Phosphoprotein-binding domains interact with cognate phosphorylated targets ruling several biological processes. The impairment of such interactions is often associated with disease development, namely cancer. The breast cancer susceptibility gene 1 (BRCA1) C-terminal (BRCT) domain is involved in the control of complex signaling networks of the DNA damage response. The capture and identification of BRCT-binding proteins and peptides may be used for the development of new diagnostic tools for diseases with abnormal phosphorylation profiles. Here we show that designed cyclic β-hairpin structures can be used as peptidomimetics of the BRCT domain, with high selectivity in binding to a target phosphorylated peptide. The amino acid residues and spatial constraints involved in the interaction between a phosphorylated peptide (GK14-P) and the BRCT domain were identified and crafted onto a 14-mer β-hairpin template in silico. Several cyclic peptides models were designed and their binding towards the target peptide and other phosphorylated peptides evaluated through virtual screening. Selected cyclic peptides were then synthesized, purified and characterized. The high affinity and selectivity of the lead cyclic peptide towards the target phosphopeptide was confirmed, and the possibility to capture it using affinity chromatography demonstrated. This work paves the way for the development of cyclic β-hairpin peptidomimetics as a novel class of affinity reagents for the highly selective identification and capture of target molecules.

The effect of turn residues on the folding and cell-penetrating activity of β-hairpin peptides and applications toward protein delivery

Cell-penetrating peptides (CPPs) are useful tools for the delivery of a wide variety of cargo into cells. Our lab has developed two classes of CPPs based on β-hairpin sequences, one that folds at the surface of cell membranes and the other that is intrinsically disordered. Although these peptides can effectively deliver different types of cargo, their use in protein delivery has been hindered due to the presence of non-natural D-proline within the central turn region of both sequences, which prohibits functionalizing proteins with the CPPs via standard expression protocols. In this work, we describe new CPPs that replace the non-natural turn region with natural turn motifs amenable to protein expression. We first investigate how these changes within the turn affect various CPP-related properties in the absence of protein cargo, and then generate protein fusions for intracellular delivery.

From phage display to structure: an interplay of enthalpy and entropy in the binding of the LDHSLHS polypeptide to silica

Polypeptide based biosilica composites show promise as next generation multi-functional nano-platforms for diagnostics and bio-catalytic applications. Following the identification of a strong silica binder (LDHSLHS) by phage display, we conduct structural analysis of the polypeptide at the interface with amorphous silica nanoparticles in an aqueous environment. Our approach relies on modelling infrared and Raman spectral responses using predictions of molecular dynamics simulations and quantum studies of the normal modes for several potential structures. By simultaneously fitting both infrared and Raman responses in the amide spectral region, we show that the main structural conformer has a beta-like central region and helix-twisted terminals. Classical simulations, as conducted previously (Chem. Mater., 2014, 26, 5725), predict that the association of the main structure with the interface is stimulated by electrostatic interactions though surface binding also requires spatially distributed sodium ions to compensate for negatively charged acidic silanol groups. Accordingly, diffusion of sodium ions would contribute to a stochastic character of the peptide association with the surface. Consistent with the described dynamics at the interface, the results obtained from isothermal titration calorimetry (ITC) confirm a significant enhancement of polypeptide binding to silica at higher concentrations of Na+. The results of this study suggest that the tertiary structure of a phage capsid protein plays a significant role in regulating the conformation of peptide LDHSLHS, increasing its binding to silica during the phage display process. The results presented here support design-led engineering of polypeptide-silica nanocomposites for bio-technological applications.

Aromatic interactions in β-hairpin scaffold stability: A historical perspective

Non-covalent interactions between naturally occurring aromatic residues have been widely exploited as scaffold stabilizing agents in de novo designed peptides and in Nature - inspired structures. Our understanding of the factors driving aromatic interactions and their observed interaction geometries have advanced remarkably with improvements in conventional structural studies, availability of novel molecular methods and in silico studies, which have together provided atomistic information on aromatic interactions and interaction strengths. This review attempts to recapitulate the early advances in our understanding of aromatic interactions as stabilizing agents of peptide β-hairpins.

Molecular Dynamics Simulations of a Conformationally Mobile Peptide-Based Catalyst for Atroposelective Bromination

It is widely accepted that structural rigidity is required to achieve high levels of asymmetric induction in catalytic, enantioselective reactions. This fundamental design principle often does not apply to highly selective catalytic peptides that often exhibit conformational heterogeneity. As a result, these complex systems are particularly challenging to study both experimentally and computationally. Herein, we utilize molecular dynamics simulations to investigate the role of conformational mobility on the reactivity and selectivity exhibited by a catalytic, β-turn-biased peptide in an atroposelective bromination reaction. By means of cluster analysis, multiple distinct conformers of the peptide and a catalyst-substrate complex were identified in the simulations, all of which were corroborated by experimental NMR measurements. The simulations also revealed that a shift in the conformational equilibrium of the peptidic catalyst occurs upon addition of substrate, and the degree of change varies among different substrates. On the basis of these data, we propose a correlation between the composition of the peptide conformational ensemble and its catalytic properties. Moreover, these findings highlight the importance of conformational dynamics in catalytic, asymmetric reactions mediated by oligopeptides, unveiled through high-level, state-of-the-art computational modeling.

A Two-Tailed Phosphopeptide Crystallizes to Form a Lamellar Structure

The crystal structure of a designed phospholipid-inspired amphiphilic phosphopeptide at 0.8 Å resolution is presented. The phosphorylated β-hairpin peptide crystallizes to form a lamellar structure that is stabilized by intra- and intermolecular hydrogen bonding, including an extended β-sheet structure, as well as aromatic interactions. This first reported crystal structure of a two-tailed peptidic bilayer reveals similarities in thickness to a typical phospholipid bilayer. However, water molecules interact with the phosphopeptide in the hydrophilic region of the lattice. Additionally, solid-state NMR was used to demonstrate correlation between the crystal structure and supramolecular nanostructures. The phosphopeptide was shown to self-assemble into semi-elliptical nanosheets, and solid-state NMR provides insight into the self-assembly mechanisms. This work brings a new dimension to the structural study of biomimetic amphiphilic peptides with determination of molecular organization at the atomic level.

Diversity of Secondary Structure in Catalytic Peptides with β-Turn-Biased Sequences

X-ray crystallography has been applied to the structural analysis of a series of tetrapeptides that were previously assessed for catalytic activity in an atroposelective bromination reaction. Common to the series is a central Pro-Xaa sequence, where Pro is either l- or d-proline, which was chosen to favor nucleation of canonical β-turn secondary structures. Crystallographic analysis of 35 different peptide sequences revealed a range of conformational states. The observed differences appear not only in cases where the Pro-Xaa loop-region is altered, but also when seemingly subtle alterations to the flanking residues are introduced. In many instances, distinct conformers of the same sequence were observed, either as symmetry-independent molecules within the same unit cell or as polymorphs. Computational studies using DFT provided additional insight into the analysis of solid-state structural features. Select X-ray crystal structures were compared to the corresponding solution structures derived from measured proton chemical shifts, 3J-values, and 1H-1H-NOESY contacts. These findings imply that the conformational space available to simple peptide-based catalysts is more diverse than precedent might suggest. The direct observation of multiple ground state conformations for peptides of this family, as well as the dynamic processes associated with conformational equilibria, underscore not only the challenge of designing peptide-based catalysts, but also the difficulty in predicting their accessible transition states. These findings implicate the advantages of low-barrier interconversions between conformations of peptide-based catalysts for multistep, enantioselective reactions.

Crystal structure of a tripeptide containing aminocyclododecane carboxylic acid: a supramolecular twisted parallel β-sheet in crystals

The crystal structure of a tripeptide Boc-Leu-Val-Ac12 c-OMe (1) is determined, which incorporates a bulky 1-aminocyclododecane-1-carboxylic acid (Ac12 c) side chain. The peptide adopts a semi-extended backbone conformation for Leu and Val residues, while the backbone torsion angles of the C(α,α) -dialkylated residue Ac12 c are in the helical region of the Ramachandran map. The molecular packing of 1 revealed a unique supramolecular twisted parallel β-sheet coiling into a helical architecture in crystals, with the bulky hydrophobic Ac12 c side chains projecting outward the helical column. This arrangement resembles the packing of peptide helices in crystal structures. Although short oligopeptides often assemble as parallel or anti-parallel β-sheet in crystals, twisted or helical β-sheet formation has been observed in a few examples of dipeptide crystal structures. Peptide 1 presents the first example of a tripeptide showing twisted β-sheet assembly in crystals.

Nature of aryl-tyrosine interactions contribute to β-hairpin scaffold stability: NMR evidence for alternate ring geometry

The specific contribution of the acidic-aromatic β-sheet favouring amino acid tyrosine to the stability of short octapeptide β-hairpin structures is presented here. Solution NMR analysis in near-apolar environments suggests the energetically favourable mode of interaction to be T-shaped face-to-edge (FtE) and that a Trp-Tyr interacting pair is the most stabilizing. Alternate aryl geometries also exist in solution, which readily equilibrate between a preferred π···π conformation to an aromatic-amide conformation, without any change in the backbone structure. While the phenolic ring is readily accommodated at the "edge" of FtE aryl interactions, it exhibits an overall lowered contribution to scaffold stability in the "face" orientation. Such differential tyrosine interactions are key to its dual nature in proteins.

Asymmetric contribution of aromatic interactions stems from spatial positioning of the interacting aryl pairs in β-hairpins

Isolated aromatic interactions in designed octapeptide β-hairpin scaffolds display a near-universal T-shaped face-to-edge geometry in all positional permutations, with the exception of aryl-Trp interactions. The heterogeneous asymmetric indole ring of Trp competes for a "shielding" face geometry, which lowers the scaffold stability in FtE aryl-Trp pairs. Assessment of the contributions of aryl pairs (in the absence of solvent-driven interactions) to the overall β-hairpin structure reveals the superiority of Trp-Phe and Trp-Tyr contributions over the well-established scaffold stabilization by Trp-Trp.

Comparative analysis of cross strand aromatic–Phe interactions in designed peptide β-hairpins

Examination of the preferential interaction geometries of the aromatic amino acids Phe, Tyr and Trp with the benzyl ring of Phe in designed octapeptide hairpin scaffolds reveals stabilizing contributions of a Trp–Phe pair, even in amphipathic solvents.

Peptide turns through just ‘one atom’! A sulfamide group nucleates folding and stabilizes new supramolecular topologies in short peptides

Peptide segments with centrally placed sulfamide groups showed a remarkable tendency to adopt a turn conformation and exhibited supramolecular topologies like ‘helical stacks’ and ‘hairpin sheets’ through a highly coordinated array of strong and weak hydrogen bonds.