[Show abstract][Hide abstract] ABSTRACT: Peptaibiotics are a group of membrane active peptides of fungal origin. They typically contain α-aminoisobutyric acid (Aib; 1-letter code, U) and other non-coded residues (Toniolo and Brückner, 2009; Neumann et al., 2015; Benedett et al., 1982) [1–3] stabilizing their helical structure. Peptaibols are peptaibiotics carrying a 1, 2-aminoalcohol at the C-terminus. When a fatty acid chain (of 8–10 carbon atoms) is present at their N-terminus, they are called lipopeptaibols (Toniolo et al., 2001; Degenkolb et al., 2003) [4,5]. We found (Tavano et al., 2015)  that the lipopeptaibol trichogin displays no antibacterial effects up to 64µM, against both Gram− and Gram+ bacteria, but kills tumor and healthy human cells via a mechanism requiring both the C-terminal primary alcohol group and the N-terminal n-octanoyl moiety, with EC50s around 4–5µM. However, the substitution of single Gly residues with Lys strongly improves anti-Gram+ activity (Tavano et al., 2015; De Zotti, Biondi, Park et al., 2012; De Zotti, Biondi, Peggion et al., 2012) [6–8]. To further characterize the activity of trichogin analogs as antibiotics and cytotoxic agents, we here manipulated the peptide helix amphipathicity by means of two different substitutions: (i) Aib to Leu (De Zotti et al., 2012)  or (ii) multiple Gly to Lys changes (Tavano et al., 2015; De Zotti, Biondi, Park et al., 2012; De Zotti, Biondi, Peggion, Formaggio et al., 2012; De Zotti, Biondi, Peggion, De Poli et al., 2012) [6–9]. The antibacterial activity against four commensal or opportunistic bacterial species and the cytotoxicity against a panel of 9 healthy and tumor-derived eukaryotic cell types (including erythrocytes) are reported as MIC and EC50 (MTS - [3-(4, 5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)]-2H-tetrazolium- reduction and LDH - lactate dehydrogenase - release assay).
[Show abstract][Hide abstract] ABSTRACT: This chapter is an update of our contribution on the same topic published 20 years ago which dealt with the important issue of our still incomplete understanding of the reaction mechanisms involved in peptide bond formation and their implications for reactivity, regiospecificity, and propensity to racemize (or epimerize). The electronic and steric properties of five classes of C-carboxyl reactive derivatives of a-amino acid and peptides, namely fluorides, anhydrides, esters, azides, and amides are reviewed on the basis of the available 3D-structure information, mainly extracted from detailed X-ray diffraction analyses.
[Show abstract][Hide abstract] ABSTRACT: The properties of antimicrobial peptides adsorbed on inorganic or organic surfaces are of interest for their potential applications in intracellular drug delivery. In this work, continuous-wave (CW) electron paramagnetic resonance (EPR) and pulsed electron-electron double resonance (PELDOR) techniques were applied to study adsorption of the short-sequence trichogin GA IV and the medium-length sequence ampullosporin A antimicrobial peptides on the monodisperse colloidal silica nanospheres of 20 nm diameter. The results obtained by CW EPR support the view that the adsorbed peptides form close-packed clusters. PELDOR data show that both trichogin and ampullosporin adsorbed on the silica surface possess a more disordered conformation as compared to that in solution. For ampullosporin, disordering is much more pronounced than for trichogin. After desorption, the peptides restored their conformations; upon adsorption the peptides in some cases may lose partly their biradical character.
No preview · Article · Dec 2015 · Applied Magnetic Resonance
[Show abstract][Hide abstract] ABSTRACT: Ampullosporin A is a medium-length (14-amino acid long) hydrophobic peptide of the peptaibol family. In this work, electron paramagnetic resonance and circular dichroism spectroscopies were applied to study the interaction of synthetic ampullosporin A and three spin-labeled analogs with small unilamellar vesicles and bicelles. Zwitterionic vesicles were used to investigate the conformation and the penetration depth of the peptide at room temperature. Bicelles were employed in combination with EPR spectroscopy to study the order, dynamics, orientation, aggregation and the 3D-structure of the peptide at near physiological temperature. In the membrane, the peptide adopts a helical structure that changes in nature depending on the thickness of the membrane-mimetic system, from mostly α-helical in vesicles to a more elongated helix in bicelles, suggesting an increase in the 310-helical content. The orientation assumed by the peptide also shows a dependence on the membrane-mimetic system: in bicelles, ampullosporin A has a transmembrane orientation at a peptide-to-lipid (P : L) ratio of 1 : 100 and higher, while in vesicles it undergoes a transition from a parallel to a transmembrane orientation as a function of the P : L ratio. In bicelles, the peptide was found to be monomeric at a P : L ratio of 1 : 25 and lower. Overall, the comparison of the results obtained in the two membrane-mimetic systems showed that ampullosporin A has a rather flexible structure that readily adapts to the bilayer thickness.
No preview · Article · Dec 2015 · Physical Chemistry Chemical Physics
[Show abstract][Hide abstract] ABSTRACT: A helical hexapeptide was designed to link in a rigid parallel orientation to a gold surface. The peptide sequence of the newly synthesized compound is characterized by the presence of two 4-amino-1,2-dithiolane-4-carboxylic acid (Adt) residues (positions 1 and 4) to promote a bidentate interaction with the gold surface, two L-Ala residues (positions 2 and 5) and two-aminoisobutyric acid (Aib) residues (positions 3 and 6) to favor a high population of the 310-helix conformation. Furthermore, a ferrocenoyl (Fc) probe was inserted at the N-terminus to investigate the electronic conduction properties of the peptide. X-Ray Photoelectron Spectroscopy and Scanning Tunneling Microscopy techniques were used to characterize the binding of the peptide to the gold surface and the morphology of the peptide layer, respectively. Several electrochemical (Cyclic Voltammetry, Chronoamperometry, Square Wave Voltammetry) techniques were applied to analyze the electrochemical activity of the Fc probe, along with the influence of the peptide 3D-structure and the peptide layer morphology on electron transfer processes.
[Show abstract][Hide abstract] ABSTRACT: A dual-action ligand targeting both integrin αVβ3 and vascular endothelial growth factor receptors (VEGFRs), was synthesized via conjugation of a cyclic peptidomimetic αVβ3 Arg-Gly-Asp (RGD) ligand with a decapentapeptide. The latter was obtained from a known VEGFR antagonist by acetylation at the Lys13 side chain. Functionalization of the precursor ligands was carried out in solution and in the solid phase, affording two fragments: an alkyne VEGFR ligand and the azide integrin αVβ3 ligand, which were conjugated by click chemistry. Circular dichroism studies confirmed that both the RGD and VEGFR ligand portions of the dual-action compound substantially adopt the biologically active conformation. In vitro binding assays on isolated integrin αVβ3 and VEGFR-1 showed that the dual-action conjugate retains a good level of affinity for both its target receptors, although with one order of magnitude (10/20 times) decrease in potency. The dual-action ligand strongly inhibited the VEGF-induced morphogenesis in Human Umbilical Vein Endothelial Cells (HUVECs). Remarkably, its efficiency in preventing the formation of new blood vessels was similar to that of the original individual ligands, despite the worse affinity towards integrin αVβ3 and VEGFR-1.
[Show abstract][Hide abstract] ABSTRACT: We have used a combination of 2D IR spectroscopy with 13C═18O labeled amide-I and 15N-labeled amide-II modes to reveal how vibrational coupling between labeled peptide units depends on secondary structure. Linear and 2D IR measurements and simulations of Cα,α-diethylglycine homotetrapeptide show that this compound adopts the fully extended (2.05-helical) conformation in CDCl3, consistent with previous work on the Ac-capped peptide. The amide-I/II cross peaks of isotopomers exhibit only a marginal isotope frequency shift between labeled modes that are separated by two peptide units, indicating a very weak coupling. This result is in sharp contrast with a large cross-peak shift observed in 310-helical peptides, in which the labeled amide-I and -II modes are connected through an inter-residue C═O···H-N hydrogen bond. The discovered 3D-structural dependence indicates that the 13C═18O/15N labeled amide-I/II cross peaks can distinguish the formation of a single 310-helical turn from the fully extended polypeptide chain and increase the versatility of 2D IR spectroscopy as a conformational analysis tool of biomolecules.
No preview · Article · Dec 2014 · The Journal of Physical Chemistry C
[Show abstract][Hide abstract] ABSTRACT: In contrast to the extensively investigated β-turn conformation in peptides and proteins, single and multiple γ-turns have been poorly studied. Single and non-contiguous multiple γ-turns have been relatively often authenticated in small cyclic peptides, but these important peptide main-chain reversal motifs have been examined carefully neither in linear peptides nor in globular proteins. This Perspective article summarizes literature data on this aspect of peptide stereochemistry, expanding the discussion also to the rarely found, contiguous multiple γ-turns which generate incipient or fully-developed 2.27-(γ-) helices. Unpublished results of recent research activities on this topic ongoing in our laboratories are also briefly outlined.
No preview · Article · Nov 2014 · New Journal of Chemistry
[Show abstract][Hide abstract] ABSTRACT: Peptaibiotics, non-ribosomally synthetized peptides from various ascomycetes, are uniquely characterized by di-alkylated α-amino acids, a rigid helical conformation, and membrane permeation properties. Although generally considered antimicrobial peptides, peptaibiotics may display other toxicological properties, and their function is in many cases unknown. With the goal to define the biological activity and selectivity of the peptaibiotic trichogin GA IV from the human opportunist Trichomonas longibrachiatum we analyzed its membrane interaction, cytotoxic activity and antibacterial effect. Trichogin GA IV effectively killed several types of healthy and neoplastic human cells at doses (EC50%=4-6μM) lacking antibiotic effects on both Gram(-) and Gram(+) bacteria (MIC>64μM). The peptaibiotic distinctive C-terminal primary alcohol was found to cooperate with the N-terminal n-octanoyl group to permeate the membrane phospholipid bilayer and to mediate effective binding and active endocytosis of trichogin GA IV in eukaryotic cells, two steps essential for cell death induction. Replacement of one Gly with Lys plus the simultaneous esterification of the C-terminus, strongly increased trichogin GA IV anti-Gram(+) activity (MIC 1-4μM), but further mitigated its cytotoxicity on human cells.
Full-text · Article · Oct 2014 · Biochimica et Biophysica Acta (BBA) - Biomembranes
[Show abstract][Hide abstract] ABSTRACT: We prepared, by solution-phase methods, and fully characterized three analogs of the membrane-active peptaibiotic alamethicin F50/5, bearing a single trifluoroacetyl (Tfa) label at the N-terminus, at position 9 (central region) or at position 19 (C-terminus), and with the three Gln at positions 7, 18, and 19 replaced by Glu(OMe) residues. To add the Tfa label at position 9 or 19, a γ-trifluoroacetylated α,γ-diaminobutyric acid (Dab) residue was incorporated as a replacement for the original Val(9) or Glu(OMe)(19) amino acid. We performed a detailed conformational analysis of the three analogs (using FT-IR absorption, CD, 2D-NMR, and X-ray diffraction), which clearly showed that Tfa labeling does not introduce any dramatic backbone modification in the predominantly α-helical structure of the parent peptaibiotic. The results of an initial solid-state (19) F-NMR study on one of the analogs favor the conclusion that the Tfa group is a very promising reporter for the analysis of peptaibioticmembrane interactions. Finally, we found that the antimicrobial activities of the three newly synthesized analogs depend on the position of the Tfa label in the peptide sequence.
No preview · Article · Aug 2014 · Chemistry & Biodiversity
[Show abstract][Hide abstract] ABSTRACT: Oxo-dipeptides and thio-dipeptides are built via condensation between couples of amino acids and amino thioacids, the latter with the carbonyl oxygen replaced by an sp(2) sulfur. We explored via in silico methods (PBE0/6-31G(d,p) and PBE0/6-311G(d,p)) all the possible combinations and built 800 dipeptides, whose structures were fully optimized. Maps of condensation energies are presented to highlight optimal partners leading to stable dipeptides and critical situations for which lower stability or instability is predicted in terms of Gibbs reaction free energies. To validate the feasibility of our computational investigation, we synthesized and compared the stabilities of two thionated dimers, namely -Gly[Ψ(CSNH)]Gly- and -Phe[Ψ(CSNH)]Phe-, characterized by diverging physico-chemical properties. To the best of our knowledge, this is the first systematic analysis reported for dipeptides built from natural amino acids as well as for their corresponding thio-analogs.
No preview · Article · Jul 2014 · Physical Chemistry Chemical Physics
[Show abstract][Hide abstract] ABSTRACT: Trichogin GA IV, an antimicrobial peptaibol, exerts its function by augmenting membrane permeability, but the molecular aspects of its pore-forming mechanism are still debated. Several lines of evidence indicate a ‘barrel-stave’ channel structure, similar to that of alamethicin, but the length of a trichogin helix is too short to span a normal bilayer. Herein, we present electrophysiology measurements in planar bilayers, showing that trichogin does form channels of a well-defined size (R=4.2⋅109 Ω; corresponding at least to a trimeric aggregate) that span the membrane and allow ion diffusion, but do not exhibit voltage-dependent rectification, unlike those of alamethicin.
[Show abstract][Hide abstract] ABSTRACT: The PELDOR technique was used to obtain the spectra of distances between spin labels for mono and double TOAC substituted analogues of [Glu(OMe)(7,18,19)] alamethicin F50/5 (Alm') peptaibiotic on the surface of the organic sorbent Oasis HLB and in ethanol solution at 77 K. For the double-labeled Alm', the free radical probes are at positions 1 and 16 (Alm'1,16). The intra- and intermolecular contributions to the PELDOR time traces were separated, with regard to the fractality of the system studied. We established that on HLB the labeled Alm' molecules are prone to aggregation. The distance spectra for Alm'1,16 show that, in both adsorbed state and in ethanol solution, the peptaibiotic is predominantly folded in the α-helix conformation. We assign the asymmetry of the distance spectrum in both cases to the occurrence of an admixture of more elongated α/310-helical conformers. The portion of these conformers is higher for the peptide adsorbed on HLB. We speculate that both the broadening of the basic spectrum line at rmax = 2.0 nm and the increase in the contribution of elongated conformers might be associated with the spread of the peptaibiotic adsorption sites on HLB as compared with the more uniform Alm'1,16 trap structure in frozen ethanol solution. The aggregates of mono-labeled Alm'1 and Alm'16 also studied. The intermolecular distance spectrum for Alm'1 on HLB is shifted toward longer distances as compared with those of Alm'16. This result suggests that in the aggregates Alm' molecules are preferentially oriented with their C-terminal regions in the vicinity.
No preview · Article · Jun 2014 · The Journal of Physical Chemistry B
[Show abstract][Hide abstract] ABSTRACT: Photoinduced electron transfer (PET) experiments have been carried out on peptide self-assembled monolayers (SAM) chemisorbed on a gold substrate. The oligopeptide building block was exclusively formed by Cα-tetrasubstituted α-aminoisobutyric residues to attain a helical conformation despite the shortness of the peptide chain. Furthermore, it was functionalized at the C-terminus by a pyrene chromophore to enhance the UV photon capture cross-section of the compound and by a lipoic group at the N-terminus for linking to gold substrates. Electron transfer across the peptide SAM has been studied by photocurrent generation experiments in an electrochemical cell employing a gold substrate modified by chemisorption of a peptide SAM as a working electrode and by steady state and time-resolved fluorescence experiments in solution and on a gold-coated glass. The results show that the electronic flow through the peptide bridge is strongly asymmetric, i.e. PET from the C-terminus to gold is highly favored with respect to PET in the opposite direction. This effect arises from the polarity of the Au-S linkage (Auδ+-Sδ-, junction effect) and from the electrostatic field generated by the peptide helix.
Full-text · Article · Jun 2014 · The Journal of Physical Chemistry A