Synthesis of homopolypeptides with PPII structure

Proline Analogues

Within the canonical repertoire of the amino acid involved in protein biogenesis, proline plays a unique role as an amino acid presenting a modified backbone rather than a side-chain. Chemical structures that mimic proline but introduce changes into its specific molecular features are defined as proline analogues. This review article summarizes the existing chemical, physicochemical, and biochemical knowledge about this peculiar family of structures. We group proline analogues from the following compounds: substituted prolines, unsaturated and fused structures, ring size homologues, heterocyclic, e.g., pseudoproline, and bridged proline-resembling structures. We overview (1) the occurrence of proline analogues in nature and their chemical synthesis, (2) physicochemical properties including ring conformation and cis/trans amide isomerization, (3) use in commercial drugs such as nirmatrelvir recently approved against COVID-19, (4) peptide and protein synthesis involving proline analogues, (5) specific opportunities created in peptide engineering, and (6) cases of protein engineering with the analogues. The review aims to provide a summary to anyone interested in using proline analogues in systems ranging from specific biochemical setups to complex biological systems.

Bilayer thickness determines the alignment of model polyproline helices in lipid membranes

Our understanding of protein folds relies fundamentally on the set of secondary structures found in the proteomes. Yet, there also exist intriguing structures and motifs that are underrepresented in natural biopolymeric systems. One example is the polyproline II helix, which is usually considered to have a polar character and therefore does not form membrane spanning sections of membrane proteins. In our work, we have introduced specially designed polyproline II helices into the hydrophobic membrane milieu and used 19F NMR to monitor the helix alignment in oriented lipid bilayers. Our results show that these artificial hydrophobic peptides can adopt several different alignment states. If the helix is shorter than the thickness of the hydrophobic core of the membrane, it is submerged into the bilayer with its long axis parallel to the membrane plane. The polyproline helix adopts a transmembrane alignment when its length exceeds the bilayer thickness. If the peptide length roughly matches the lipid thickness, a coexistence of both states is observed. We thus show that the lipid thickness plays a determining role in the occurrence of a transmembrane polyproline II helix. We also found that the adaptation of polyproline II helices to hydrophobic mismatch is in some notable aspects different from α-helices. Finally, our results prove that the polyproline II helix is a competent structure for the construction of transmembrane peptide segments, despite the fact that no such motif has ever been reported in natural systems.

Transmembrane Polyproline Helix

The third most abundant polypeptide conformation in nature, the polyproline-II helix, is a polar, extended secondary structure with a local organization stabilized by intercarbonyl interactions within the peptide chain. Here we design a hydrophobic polyproline-II helical peptide based on an oligomeric octahydroindole-2-carboxylic acid scaffold and demonstrate its transmembrane alignment in model lipid bilayers by means of solid-state ¹⁹F NMR. As result, we provide a first example of a purely artificial transmembrane peptide with a structural organization that is not based on hydrogen-bonding.

Exploring hydrophobicity limits of polyproline helix with oligomeric octahydroindole-2-carboxylic acid

The polyproline-II helix is the most extended naturally occurring helical structure and is widely present in polar, exposed stretches and "unstructured" denatured regions of polypeptides. Can it be hydrophobic? In this study, we address this question using oligomeric peptides formed by a hydrophobic proline analogue, (2S,3aS,7aS)-octahydroindole-2-carboxylic acid (Oic). Previously, we found the molecular principles underlying the structural stability of the polyproline-II conformation in these oligomers, whereas the hydrophobicity of the peptide constructs remains to be examined. Therefore, we investigated the octan-1-ol/water partitioning and inclusion in detergent micelles of the oligo-Oic peptides. The results showed that the hydrophobicity is remarkably enhanced in longer oligomeric sequences, and the oligo-Oic peptides with 3 to 4 residues and higher are specific towards hydrophobic environments. This contrasts significantly to the parent oligoproline peptides, which were moderately hydrophilic. With these findings, we have demonstrated that the polyproline-II structure is compatible with nonpolar media, whereas additional manipulations of the terminal functionalities feature solubility in extremely nonpolar solvents such as hexane.