Secondary conformation of short lysine- and leucine-rich peptides assessed by optical spectroscopies: effect of chain length, concentration, solvent, and time

The relationship between the tyrosine residue 850-830 cm-1 Raman doublet intensity ratio and the aromatic side chain χ1 torsion angle

Tyrosine (Tyr) residue in a peptide chain is characterized by the presence of seven Raman markers, referred to as Yi (i = 1, …, 7), distributed over the middle wavenumber spectral region. Particularly, the changes observed in the relative intensity of Y5 and Y6 markers, appearing as a side by side doublet at ca. 850-830 cm-1, has received a great attention. Primarily assigned to a Fermi-resonance effect between phenol ring planar and nonplanar modes, former density functional theory calculations led us to affiliate the Y5-Y6 doublet to two distinct fundamental modes. Furthermore, despite the previous assumptions, it was evidenced that the reversal of the doublet intensity ratio cannot be solely explained by hydrogen bonding on the phenol hydroxyl group involved in Tyr. Herein, upon analyzing the observed and theoretical data collected from the cationic species of the tripeptide Gly-Tyr-Gly, the crucial effect of the aromatic side chain orientation, especially that of the χ1 torsion angle defined around the CαCβ bond, on the Tyr doublet intensity ratio has been evidenced.

Antibiotic Potential and Biophysical Characterization of Amphipathic β-Stranded [XZ]n Peptides With Alternating Cationic and Hydrophobic Residues

Cationic membrane-active peptides are considered to be promising candidates for antibiotic treatment. Many natural and artificial sequences show an antimicrobial activity when they are able to take on an amphipathic fold upon membrane binding, which in turn perturbs the integrity of the lipid bilayer. Most known structures are α-helices and β-hairpins, but also cyclic knots and other irregular conformations are known. Linear β-stranded antimicrobial peptides are not so common in nature, but numerous model sequences have been designed. Interestingly, many of them tend to be highly membranolytic, but also have a significant tendency to self-assemble into β-sheets by hydrogen-bonding. In this minireview we examine the literature on such amphipathic peptides consisting of simple repetitive sequences of alternating cationic and hydrophobic residues, and discuss their advantages and disadvantages. Their interactions with lipids have been characterized with a number of biophysical techniques—especially circular dichroism, fluorescence, and infrared—in order to determine their secondary structure, membrane binding, aggregation tendency, and ability to permeabilize vesicles. Their activities against bacteria, biofilms, erythrocytes, and human cells have also been studied using biological assays. In line with the main scope of this Special Issue, we attempt to correlate the biophysical results with the biological data, and in particular we discuss which properties (length, charge, aggregation tendency, etc.) of these simple model peptides are most relevant for their biological function. The overview presented here offers ideas for future experiments, and also suggests a few design rules for promising β-stranded peptides to develop efficient antimicrobial agents.

Phosphate-dependent aggregation of [KL]n peptides affects their membranolytic activity

In this study, we investigate how the length of amphiphilic β-sheet forming peptides affects their interaction with membranes. Four polycationic model peptides with lengths from 6 to 18 amino acids were constructed from simple Lys-Leu repeats, giving [KL]_n=3,5,7,9. We found that (1) they exhibit a pronounced antimicrobial activity with an intriguing length dependent maximum for [KL]₅ with 10 amino acids; (2) their hemolytic effect, on the other hand, increases steadily with peptide length. CD analysis (3) and TEM (4) show that all peptides-except for the short [KL]₃-aggregate into amyloid-like fibrils in the presence of phosphate ions, which in turn has a critical effect on the results in (1) and (2). In fact, (5) vesicle leakage reveals an intrinsic membrane-perturbing activity (at constant peptide mass) of [KL]₅ > [KL]₉ > [KL]₇ in phosphate buffer, which changes to [KL]₅ ≈ [KL]₇ ≈ [KL]₉ in PIPES. A specific interaction with phosphate ions thus explains the subtle balance between two counteracting effects: phosphate-induced unproductive pre-aggregation in solution versus monomeric membrane binding and vigorous lipid perturbation due to self-assembly of the bound peptides within the bilayer. This knowledge can now be used to control and optimize the peptides in further applications.

Structural Analysis of Nonapeptides Derived from Elastin

Elastin-derived peptides are released from the extracellular matrix remodeling by numerous proteases and seem to regulate many biological processes, notably cancer progression. The canonical elastin peptide is VGVAPG, which harbors the XGXXPG consensus pattern, allowing interaction with the elastin receptor complex located at the surface of cells. Besides these elastokines, another class of peptides has been identified. This group of bioactive elastin peptides presents the XGXPGXGXG consensus sequence, but the reason for their bioactivity remains unexplained. To better understand their nature and structure-function relationships, herein we searched the current databases for this nonapeptide motif and observed that the XGXPGXGXG elastin peptides define a specific group of tandemly repeated patterns. Further, we focused on four tandemly repeated human elastin nonapeptides, i.e., AGIPGLGVG, VGVPGLGVG, AGVPGLGVG, and AGVPGFGAG. These peptides were analyzed by means of optical spectroscopies and molecular dynamics. Ultraviolet-circular dichroism and Raman spectra are consistent with a mixture of β-turn, β-strand, and random-chain secondary elements in aqueous media. Quantitative analysis of their conformations suggested that turns corresponded to half of the total population of structural elements, whereas the remaining half were equally distributed between β-strand and unordered chains. These distributions were confirmed by molecular dynamics simulations. Altogether, our data suggest that these highly dynamic peptides harbor a type II β-turn located in their central part. We hypothesize that this structural element could explain their specific bioactivity.

Disorder-to-Order Markers of a Cyclic Hexapeptide Inspired from the Binding Site of Fertilin β Involved in Fertilization Process

Synthetic peptides mimicking the binding site of fertilin β to its receptor, integrin α6β1, were shown to inhibit sperm-egg fusion when added to in vitro media. In contrast, the synthetic cyclic hexapeptide, cyclo(Cys¹-Ser²-Phe³-Glu⁴-Glu⁵-Cys⁶), named as cFEE, proved to stimulate gamete fusion. Owing to its biological specificity, this hexapeptide could help improve the in vitro fertilization pregnancy rate in human. In an attempt to establish the structure-activity relationship of cFEE, its structural dynamics was herein analyzed by means of ultraviolet circular dichroism (UV-CD) and Raman scattering. The low concentration CD profile in water, containing mainly a deep minimum at ∼202 nm, is consistent with a rather unordered chain. However, an ordering trend of the peptide loop has been observed in a less polar solvent such as methanol, where the UV-CD signal shape is formed by a double negative marker at ∼202/215 nm, indicating the presence of a type-II' β-turn. Raman spectra recorded in aqueous samples upon a 100-fold concentration increase, still showed an important population (∼30%) of the disordered structure. The structural flexibility of the disulfide bridge was confirmed by the Raman markers arising from the Cys¹-Cys⁶ disulfide bond-stretch motions. Density functional theory calculations highlighted the formation of the type-II' β-turn on the four central residues of cFEE (i.e., -Ser²-Phe³-Glu⁴-Glu⁵-) either with a left- or with a right-handed disulfide. The structure with a left-handed S-S bond, however, appears to be more stable.

Diverse Bilayer Morphologies Achieved via α-Helix-to-β-Sheet Transitions in a Short Amphiphilic Peptide

Transmembrane proteins are functional macromolecules that direct the flow of small molecules and ions across a lipid bilayer. Here, we propose the development of helical peptide amphiphiles that will serve as both the bilayer and the functional unit of a self-assembled peptide bilayer membrane. The peptide, K₃L₁₂, was designed not only to possess dimensions similar to that of a lipid bilayer but also to yield a structurally robust, α-helical bilayer. The formation of α-helices is pH-dependent, and upon annealing the sample, a transition from α-helices to β-sheets can be controlled, as indicated by optical and vibrational spectroscopies. Imaging the materials confirms morphologies similar to that of a lipid bilayer but rich in α-helices. Annealing the samples yields a shift in the morphology from bilayers to curled disks, fibers, and sheets. The structural robustness of the material can facilitate the incorporation of many functions into the bilayer assembly.

Dynamical Behavior of Somatostatin-14 and Its Cyclic Analogues as Analyzed in Bulk and on Plasmonic Silver Nanoparticles

Primarily known as the inhibitor of growth hormone release, the role of somatostatin in many other inhibiting activities upon binding to its five G-protein-coupled receptors has been elucidated. Because of the short half-life of somatostatin, a number of synthetic analogues were elaborated for this peptide hormone. Herein, after recalling the main somatostatin therapeutic interests, we present the dynamical behavior of somatostatin-14 and its two currently used synthetic cyclic analogues, octreotide and pasireotide. Physical techniques, such as fluorescence, UV-visible absorption, circular dichroism, Raman spectroscopy, surface-enhanced Raman spectroscopy, and transmission electron microscopy, were jointly used in order to get information on the solution structural features, as well as on the anchoring sites of the three peptides on silver colloids. While somatostatin-14 adopts a rather unordered chain within the submillimolar concentration range, its cyclic analogues were revealed to be ordered, i.e., stabilized either in a type-II' β-turn (octreotide) or in a face-to-face γ-turn/type-I β-turn (pasireotide) structure. Nevertheless, a progressive structuring trend was observed in somatostatin-14 upon increasing concentration to the millimolar range. Because of their cationic character, the three peptides have revealed their capability to bind onto negatively charged silver nanoparticles. The high affinity of the peptides toward metallic particles seems to be extremely promising for the elaboration of somatostatin-based functionalized plasmonic nanoparticles that can be used in diagnosis, drug delivery, and therapy.

Octreotide used for probing the type-II' β-turn CD and Raman markers

Octreotide, a potent somatostatin (SST) analogue, is used as an antiproliferative drug in numerous endocrine tumors. Previous NMR investigations, basically performed in DMSO, had evidenced a type-II' β-turn structure for this cyclic peptide. However, apart a few incomplete studies by circular dichroism, a systematic analysis of the structural behavior of octreotide in aqueous solution as a function of concentration and ionic strength was still lacking. Here, we report the chemical synthesis and purification of octreotide for optical spectroscopic purposes accompanied by its structural analysis. Furthermore, we have used octreotide as a short size, well-defined model compound for analyzing the CD and Raman markers of a type-II' β-turn. CD data collected in the 25-250 μM range revealed the general trend of octreotide to undergo a disordered toward ordered structural transition upon increasing concentration. Especially, the β-turn CD markers could be characterized above 50 μM by a negative band at ~202 nm flanked by a shoulder at ~218 nm. On the basis of Raman spectra recorded as a function of concentration (1-20 mM), we could assign the markers at ~1678 and ~1650 cm(-1) in the amide I region, and at ~1303, ~1288, and ~1251 cm(-1) in the amide III region, to the type-II' β-turn structure. The stability of the intermolecular antiparallel β-sheet formed in octreotide could be confirmed by the rigidity of the disulfide bridge which adopts a preferential gauche-gauche-gauche rotamer along the -Cβ-S-S-Cβ- moiety of the linked cysteines. The present analysis permits a better understanding of the differences between the structural features of SST-14 and its routinely used analogue, octreotide.

Vibrational analysis of amino acids and short peptides in aqueous media. V. The effect of the disulfide bridge on the structural features of the peptide hormone somatostatin-14

To emphasize the role played by the S-S bridge in the structural features of somatostatin-14 (SST-14), newly recorded CD and Raman spectra of this cyclic peptide and its open analogue obtained by Cys-->Ser substitution are presented. CD spectra of both peptides recorded in aqueous solutions in the 100-500 microM concentration range are strikingly similar. They reveal principally that random conformers constitute the major population in both peptides. Consequently, the S-S bridge has no structuring effect at submillimolar concentrations. In methanol, the CD spectrum of somatostatin-14 keeps globally the same spectral shape as that observed in water, whereas its open analogue presents a major population of helical conformers. Raman spectra recorded as a function of peptide concentration (5-20 mM) and also in the presence of 150 mM NaCl provide valuable conformational information. All Raman spectra present a mixture of random and beta-hairpin structures for both cyclic and open peptides. More importantly, the presence or the absence of the disulfide bridge does not seem to influence considerably different populations of secondary structures within this range of concentrations. CD and Raman data obtained in the submillimolar and millimolar ranges of concentrations, respectively, lead us to accept the idea that SST-14 monomers aggregate upon increasing concentration, thus stabilizing beta-hairpin conformations in solution. However, even at high concentrations, random conformers do not disappear. Raman spectra of SST-14 also reveal a concentration effect on the flexibility of the S-S linkage and consequently on that of its cyclic part. In conclusion, although the disulfide linkage does not seem to markedly influence the SST-14 conformational features in aqueous solutions, its presence seems to be necessary to ensure the flexibility of the cyclic part of this peptide and to maintain its closed structure in lower dielectric constant environments.

Vibrational analysis of amino acids and short peptides in hydrated media. IV. Amino acids with hydrophobic side chains: L-alanine, L-valine, and L-isoleucine

In the framework of our investigations on the analysis of vibrational spectra of amino acids (AAs) in hydrated media, Raman scattering and Fourier transform infrared (FT-IR) attenuated transmission reflectance (ATR) spectra of three alpha-amino acids with hydrophobic hydrocarbon side chains, i.e., alanine, valine, and isoleucine, were measured in H2O and D2O solutions. The present data complete those recently published by our group on glycine and leucine. This series of observed vibrational data gave us the opportunity to analyze the vibrational features of these amino acids in hydrated media by means of the density functional theory (DFT) calculations at the B3LYP/6-31++G* level. Harmonic vibrational modes calculated after geometry optimization on the clusters containing five water molecules interacting with H-donor and H-acceptor sites of amino acids are performed and allowed the observed main Raman and infrared bands to be assigned. Additional calculations on a cluster formed by leucine (L) and five water (W) molecules and the comparison of the obtained data with those recently published by our group on L+12W, allowed us to justify the number of hydration considered in the present report.