Hydrolysis, polarity, and conformational impact of C-terminal partially fluorinated ethyl esters in peptide models

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.

Application of (4R)-aminoproline in peptide engineering: conformational bias and pH-responsiveness revisited

How do we make proline residues pH sensitive?

Remarkably high solvatochromism in the circular dichroism spectra of the polyproline-II conformation: limitations or new opportunities?

Circular dichroism is a conventional method for studying the secondary structures of peptides and proteins and their transitions. While certain circular dichroism features are characteristic of α-helices and β-strands, the third most abundant secondary structure, the polyproline-II helix, does not exhibit a strictly conserved spectroscopic appearance. Due to its extended nature, the polyproline-II helix is highly accessible to the surrounding solvent; thus, the environment has a critical influence on the lineshape of the circular dichroism spectra of this structure. To showcase possible effects due to the medium, in this work, we report an experimental spectroscopic study of polyproline-II-forming oligomeric peptides in various environments: solvents, detergent micelles, and liposomes. Strikingly, the examination of an oligomeric peptide in a solvent series showed a remarkable 7 nm solvatochromic shift in the main negative band starting with hexafluoropropan-2-ol and moving to hexane. Furthermore, a previously predicted positive band below 200 nm was discovered in the spectra in nonpolar environments. In isotropic liposomes, the expected transition to the transmembrane state correlated with the appearance of a positive band at 228 nm. Our results demonstrate that changes in solvation should be taken into consideration when assessing the circular dichroism spectra of peptides expected to adopt the polyproline-II conformation. Although this precaution may complicate spectral analysis, characterization of solvent-induced spectral changes can generate new opportunities for testing the location of peptides in complex systems such as micelles or lipid bilayers.

Experimental lipophilicity scale for coded and noncoded amino acid residues

Among other features, the polarity of amino acid residues is the key parameter for understanding their role in proteins. The wide occurrence of protein modifications in nature and the advent of genetic code engineering techniques created a need for an experimental polarity value integrating both coded (canonical) and noncoded (noncanonical) residues on one universal scale. To address this issue, this work reports on a polarity scale based on the experimental lipophilicity of methyl esters of N-acetylamino acids. The derivatization of amino acids was performed in two steps under mild conditions that allowed conversion of a wide array of amino acids into analytical derivatives. The partitioning/distribution between octan-1-ol and water/buffer was measured using the intensity of the NMR signal as a characteristic for the concentration. The reference set of twenty coded amino acids generated log P values spanning 5.1 units: from tryptophan being the most hydrophobic to aspartate being the most hydrophilic. Furthermore, lipophilicity was measured for a set of analogues of phenylalanine, tyrosine, tryptophan, methionine, proline, and lysine that are typical in nature and/or laboratory practice. The polarity scale reported here will aid the rationalization of amino acid replacements in proteins, and will guide further efforts in experimental genetic code engineering.

Lipophilicity trends upon fluorination of isopropyl, cyclopropyl and 3-oxetanyl groups

A systematic comparison of lipophilicity modulations upon fluorination of isopropyl, cyclopropyl and 3-oxetanyl substituents, at a single carbon atom, is provided using directly comparable, and easily accessible model compounds. In addition, comparison with relevant linear chain derivatives is provided, as well as lipophilicity changes occurring upon chain extension of acyclic precursors to give cyclopropyl containing compounds. For the compounds investigated, fluorination of the isopropyl substituent led to larger lipophilicity modulation compared to fluorination of the cyclopropyl substituent.

Reconciling Electrostatic and n→π* Orbital Contributions in Carbonyl Interactions

Interactions between carbonyl groups are prevalent in protein structures. Earlier investigations identified dominant electrostatic dipolar interactions, while others implicated lone pair n→π* orbital delocalisation. Here these observations are reconciled. A combined experimental and computational approach confirmed the dominance of electrostatic interactions in a new series of synthetic molecular balances, while also highlighting the distance-dependent observation of inductive polarisation manifested by n→π* orbital delocalisation. Computational fiSAPT energy decomposition and natural bonding orbital analyses correlated with experimental data to reveal the contexts in which short-range inductive polarisation augment electrostatic dipolar interactions. Thus, we provide a framework for reconciling the context dependency of the dominance of electrostatic interactions and the occurrence of n→π* orbital delocalisation in C=O⋅⋅⋅C=O interactions.

Promotion of the collagen triple helix in a hydrophobic environment

The collagen triple helix is better suited for octanol than for water.

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.

Comparative effects of trifluoromethyl- and methyl-group substitutions in proline

What is the outcome of trifluoromethyl-/methyl-substitution in each position of the proline ring? Look inside to find out.