Fernando Formaggio

University of Padova, Padua, Veneto, Italy

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Publications (421)1188.72 Total impact

  • [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 Unpublished results of recent research activities on this topic ongoing in our laboratories are also briefly outlined.
    New Journal of Chemistry 11/2014; DOI:10.1039/C4NJ01564A · 3.16 Impact Factor
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    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.
    Biochimica et Biophysica Acta (BBA) - Biomembranes 10/2014; DOI:10.1016/j.bbamem.2014.10.005 · 3.43 Impact Factor
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    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 peptaibioticmembrane 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.
    Chemistry & Biodiversity 08/2014; 11(8):1163-91. DOI:10.1002/cbdv.201300394 · 1.80 Impact Factor
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    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.
    Physical Chemistry Chemical Physics 07/2014; DOI:10.1039/c4cp02680b · 4.20 Impact Factor
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    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.
    Chemistry & Biodiversity 07/2014; 11(7). DOI:10.1002/cbdv.201300334 · 1.81 Impact Factor
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    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.
    The Journal of Physical Chemistry B 06/2014; 118(25). DOI:10.1021/jp503691n · 3.38 Impact Factor
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    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.
    The Journal of Physical Chemistry A 06/2014; 118(33). DOI:10.1021/jp503791w · 2.78 Impact Factor
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    ABSTRACT: Three approaches for the chemical ligation of peptides to cotton fibers are described and compared. This investigation was encouraged by the need to create peptide-decorated natural textiles, furnished with useful properties (e.g. antimicrobial activity). IR absorption spectroscopy is proved to be an easy and fast method to check the covalent anchorage of a peptide to cotton, whereas for a quantitative determination, a UV absorption method was employed. We also analyzed the usefulness of electron paramagnetic resonance spectroscopy to characterize our peptide-cotton conjugates. Copyright © 2014 European Peptide Society and John Wiley & Sons, Ltd.
    Journal of Peptide Science 05/2014; 20(7). DOI:10.1002/psc.2659 · 1.86 Impact Factor
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    ABSTRACT: Interactions between peptides are relevant from a biomedical point of view, in particular for the role played by their aggregates in different important pathologies, and also because peptide aggregates represent promising scaffolds for innovative materials.In the present article, the aggregation properties of the homo-peptides formed by α-aminoisobutyric acid (U) residues are discussed. The peptides investigated have chain lengths between six and 15 residues and comprise benzyl and naphthyl groups at the N- and C-termini, respectively. Spectroscopic experiments and molecular dynamics simulations show that the shortest homo-peptide, constituted by six U, does not exhibit any tendency to aggregate under the conditions examined. On the other hand, the homologous peptide with 15 U forms very stable and compact aggregates in 70/30(v/v) methanol/water solution. Atomic force microscopy images indicate that these aggregates promote formation of long fibrils once they are deposited on a mica surface. The aggregation phenomenon is mainly due to hydrophobic interactions occurring between very stable helical structures, and the aromatic groups in the peptides seem to play a minor role. Copyright © 2014 European Peptide Society and John Wiley & Sons, Ltd.
    Journal of Peptide Science 05/2014; 20(7). DOI:10.1002/psc.2648 · 1.86 Impact Factor
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    ABSTRACT: In this article, we review the relevant results obtained during almost 60 years of research on a specific aspect of stereochemistry, namely handedness preference and switches between right-handed and left-handed helical peptide structures generated by protein amino acids or appropriately designed, side-chain modified analogs. In particular, we present and discuss here experimental and theoretical data on three categories of those screw-sense issues: (i) right-handed/left-handed α-helix transitions underwent by peptides rich in Asp, specific Asp β-esters, and Asn; (ii) comparison of the preferred conformations adopted by helical host–guest peptide series, each characterized by an amino acid residue (e.g. Ile or its diastereomer aIle) endowed with two chiral centers in its chemical structure; and (iii) right-handed (type I)/left-handed (type II) poly-(Pro)n helix transitions monitored for peptides rich in Pro itself or its analogs with a pyrrolidine ring substitution, particularly at the biologically important position 4. The unique modular and chiral properties of peptides, combined with their relatively easy synthesis, the chance to shape them into the desired conformation, and the enormous chemical diversity of their coded and non-coded α-amino acid building blocks, offer a huge opportunity to structural chemists for applications to bioscience and nanoscience problems. Copyright © 2014 European Peptide Society and John Wiley & Sons, Ltd.
    Journal of Peptide Science 05/2014; 20(5). DOI:10.1002/psc.2638 · 1.86 Impact Factor
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    ABSTRACT: The aggregation properties of two Ala-based pentapeptides were investigated by spectroscopic techniques and molecular dynamics (MD) simulations. The two peptides, both functionalized at the N-terminus with a pyrenyl group, differ in the insertion of an α-aminoisobutyric acid residue at position 4. We showed that this single modification of the homo-peptide sequence inhibits the aggregation of the pentapeptide in aqueous solutions. Atomic force microscopy imaging revealed that the two peptides form mesoscopic aggregates of very different morphologies when deposited on mica. MD experiments showed that the two peptides have a very different propensity to form β-pleated sheet structures, as confirmed by our spectroscopic measurements. The implications of these findings for our understanding of the mechanism leading to the formation of amyloid structures, primary responsible for numerous neurodegenerative diseases, are also discussed.
    Soft Matter 03/2014; 10(15):2508-19. DOI:10.1039/c3sm52831f · 4.15 Impact Factor
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    ABSTRACT: To expand the presently extremely limited repertoire of known nitronyl nitroxide α‐amino acids, we report here the synthesis of a novel, conformationally constrained, quaternary, chiral residue, Aic(CN), and its subsequent conversion into a blue‐colored, imidazolinyl nitronyl nitroxide‐bearing α‐amino acid, Aic(NN). Deprotection and peptide coupling reactions were examined. The configurational assignment of Aic(NN) was achieved by X‐ray crystallographic analysis of an appropriate tripeptide. This latter investigation, accompanied by an IR absorption conformational analysis, strongly supports the view that the Aic(NN) residue is an efficient peptide turn former. Numerous spectroscopic and magnetic properties of its derivatives and the tripeptide are also described. Of particular relevance for future applications are its UV/Vis absorption, NMR, and EPR signatures. A blue, constrained α‐amino acid bearing a sidechain imidazolinyl nitronyl nitroxide was synthesized and its spectroscopic and magnetic properties were studied. It is foreseen that this turn‐supporting residue will prove to be useful as a rigid, paramagnetic probe in peptide chemistry.
    European Journal of Organic Chemistry 03/2014; 2014(8). DOI:10.1002/ejoc.201301765 · 3.15 Impact Factor
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    ABSTRACT: Model peptides containing N-substituted 3-aminoazetidine-3-carboxylic acids have been synthesized to investigate the conformational features of these Cα-tetrasubstituted amino acids. The target peptides were designed and prepared by classical synthetic methods in solution, exploiting the convenient N-substituted 3-azidoazetidine-3-carboxylic acids as precursors. The conformational preferences of the newly synthesized peptides were investigated in solution by IR and NMR spectroscopy. It was observed that the 3-aminoazetidine-3-carboxylic acid moiety is likely a β-turn inducer. In addition, an interesting main-chain-to-side-chain hydrogen bond that forms a six-membered pseudo-cycle was detected. It connects the nitrogen (acceptor) of the azetidine ring to the amide NH (donor) of the immediately following residue. This unexpected hydrogen bond increases the number of conformational options offered by N-substituted 3-aminoazetidine-3-carboxylic acids when designing foldamers with new and predictable 3D structures.
    European Journal of Organic Chemistry 02/2014; 2014(11). DOI:10.1002/ejoc.201301741 · 3.15 Impact Factor
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    ABSTRACT: The existence of the very uncommon, but potentially quite interesting, multiple, consecutive fully-extended conformation (2.05 -helix) has been already clearly demonstrated in homo-oligopeptides based on quaternary α-amino acids with both side chains longer than methyls, but not cyclized on the α-carbon atom. To extend the scope of this research, in this work we investigated the occurrence of this flat 3D-structure in hetero-oligopeptides, each composed of two or three different residues of that class. The synthesis of a terminally protected peptide series to the tetrapeptide level was carried out by solution methods. The resulting oligomers were chemically and conformationally characterized. The data obtained point to an overwhelming population of the fully-extended conformation in CDCl3 . However, a solvent-driven switch to a predominant 310 -helical structure was seen in CD3 CN. A delicate, local balance between these two conformations is confirmed to occur in the crystalline state. Molecular dynamics simulations in CHCl3 on a hetero-tetrapeptide converged to the fully-extended conformation even starting from the 310 -helical structure.
    Biopolymers 12/2013; 102(2). DOI:10.1002/bip.22450 · 2.29 Impact Factor
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    ABSTRACT: A bioinspired approach is applied to photoelectric conversion devices. A 310 -helical hexapeptide bearing a pyrene unit is immobilized on a gold-covered TiO2 surface. The device is integrated for the first time in a dye-sensitized solar cell, exhibiting stability after several measurements. The approach could have promising applications in the field of optoelectronics.
    ChemPhysChem 11/2013; DOI:10.1002/cphc.201300901 · 3.36 Impact Factor
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    ABSTRACT: We describe the challenging solid-phase synthesis of the medium-length (14 amino-acid residues) peptaibiotic ampullosporin A, originally extracted from the fungus Sepedonium ampullosporum, and an analog doubly spin labeled (at positions 3 and 13) with the stable nitroxyl free-radical 4-amino-1-oxyl-2,2,6,6-tetramethylpiperidine-4-carboxylic acid (TOAC). The results of a circular dichrosim investigation in methanol strongly support the view that both peptides are essentially right-handed helical, in particular endowed with a large population of α-helical conformers. We also observed a significant quenching effect from the TOAC(3) nitroxyl radical on the fluorescence of Trp(1) , compatible with that expected when both residues are closely located on the same helix segment. Combined continuous wave and three-pulse PELDOR EPR methodologies converge on the conclusion obtained from the other aforementioned spectroscopies, namely that the [TOAC(3,13) ] ampullosporin A analog is mostly folded in the α-helical conformation. A liposome leakage assay demonstrated that the membrane-modifying properties of this bis-labeled analog are remarkable and even slightly superior to those of the natural peptaibiotic itself. © 2013 Wiley Periodicals, Inc. Biopolymers, 2013.
    Biopolymers 07/2013; 102(1). DOI:10.1002/bip.22362 · 2.29 Impact Factor
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    ABSTRACT: The peptide 2.05 -helix does exist. It has been experimentally authenticated both in the crystalline state (by X-ray diffraction) and in solution (by several spectroscopic techniques). It is the most common conformation for C(α) -tetrasubstituted α-amino acids with at least two atoms in each side chain, provided that cyclization on the C(α) -atom is absent. X-Ray diffraction has allowed a detailed description of its geometrical and 3D-structural features. The IR absorption and NMR parameters characteristics of this multiple, consecutive, fully-extended structure have been described. Conformational energy calculations are in agreement with the experimental findings. As the contribution per amino acid residue to the length of this helix is the longest possible, its exploitation as a molecular spacer is quite promising. However, it is a rather fragile 3D-structure and particularly sensitive to solvent polarity. Interestingly, in such a case, it may reversibly convert to the much shorter 310 -helix, thus generating an attractive molecular spring. © 2013 Wiley Periodicals, Inc. Biopolymers, 2013.
    Biopolymers 07/2013; DOI:10.1002/bip.22267 · 2.29 Impact Factor
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    ABSTRACT: Alamethicin is a 19-amino-acid residue hydrophobic peptide of the peptaibol family that has been the object of numerous studies for its ability to produce voltage-dependent ion channels in membranes. In this work, for the first time electron paramagnetic resonance spectroscopy was applied to study the interaction of alamethicin with oriented bicelles. We highlighted the effects of increasing peptide concentrations on both the peptide and the membrane in identical conditions, by adopting a twofold spin labeling approach, placing a nitroxide moiety either on the peptide or on the phospholipids. The employment of bicelles affords additional spectral resolution, thanks to the formation of a macroscopically oriented phase that allows to gain information on alamethicin orientation and dynamics. Moreover, the high viscosity of the bicellar solution permits the investigation of the peptide aggregation properties at physiological temperature. We observed that, at 35°C, alamethicin adopts a transmembrane orientation with the peptide axis forming an average angle of 25° with respect to the bilayer normal. Moreover, alamethicin maintains its dynamics and helical tilt constant at all concentrations studied. On the other hand, by increasing the peptide concentration, the bilayer experiences an exponential decrease of the order parameter, but does not undergo micellization, even at the highest peptide to lipid ratio studied (1:20). Finally, the aggregation of the peptide at physiological temperature shows that the peptide is monomeric at peptide to lipid ratios lower than 1:50, then it aggregates with a rather broad distribution in the number of peptides (from 6 to 8) per oligomer.
    Biochimica et Biophysica Acta 07/2013; DOI:10.1016/j.bbamem.2013.07.007 · 4.66 Impact Factor
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    ABSTRACT: Replacement of a peptide bond with its thioamide surrogate is a classical method for the generation of a peptidomimetic with altered spectroscopic, conformational, physicochemical, and biological properties. In this context, we synthesized short series of terminally protected homo-α-oligopeptides based on the α-amino acids Gly, Ala, and Nle, as well as their corresponding fully thioamidated analogues. For the first time, the preparation of the latter compounds was achieved in single-step fashion through direct thionation of their oxygenated precursors. Using X-ray diffraction analysis and NMR spectroscopy we were also able to confirm that the thioamidated α-amino acid residues can easily adopt either folded or fully extended conformations.
    European Journal of Organic Chemistry 06/2013; 2013(17). DOI:10.1002/ejoc.201300050 · 3.15 Impact Factor
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    ABSTRACT: In this contribution, we report on the conformational preferences of synthetic analogs of the antimicrobial peptide trichodecenin I in solution. This 6-amino acid residue long peptide is characterized by a single, strongly helicogenic Aib residue in the central part of the sequence and is rich in the conformationally mobile Gly residues. It has been reported that, in CHCl3 solution and in the crystal state, this peptaibiotic adopts a non-helical, multiple β-turn conformation, whereas a 310 /α-helical structure was obtained from an X-ray diffraction study on a trichodecenin I analog (TDT4W6) containing the fluorescent Trp residue in position 6 (replacing Ile) and an equally helicogenic TOAC residue in position 4 (replacing Aib). In this work, we applied spectroscopic techniques and molecular-dynamics calculations, in particular, on the fluorescent TDT4W6 trichodecenin I analog with the aim at investigating its 3D-structural and dynamical features in solution. Our results revealed that TDT4W6 can be described by an ensemble of conformers quickly interconverting in the nanosecond time scale. The most populated cluster has a conformation similar to the NMR structure of native trichodecenin I in CHCl3 . However, also helical-like conformers are present, even if poorly populated and less stable under the analytical conditions.
    Chemistry & Biodiversity 05/2013; 10(5):887-903. DOI:10.1002/cbdv.201200388 · 1.81 Impact Factor

Publication Stats

5k Citations
1,188.72 Total Impact Points


  • 1992–2014
    • University of Padova
      • Department of Chemical Sciences
      Padua, Veneto, Italy
  • 2000–2013
    • University of Rome Tor Vergata
      • Dipartimento di Scinze e Tecnologie Chimiche
      Roma, Latium, Italy
    • Università degli Studi di Trieste
      • Department of Chemical and Pharmaceutical Sciences
      Trst, Friuli Venezia Giulia, Italy
    • Russian Academy of Sciences
      • Institute of Chemical Kinetics and Combustion
      Moscow, Moscow, Russia
  • 1998–2012
    • National Research Council
      • • Institute of Biomolecular Chemistry ICB
      • • Laboratory of Organic Chemistry
      Roma, Latium, Italy
  • 1995–2011
    • University of Illinois at Chicago
      • Department of Chemistry
      Chicago, IL, United States
  • 2004–2010
    • Université de Versailles Saint-Quentin
      Versailles, Île-de-France, France
    • University of Michigan
      • Department of Chemistry
      Ann Arbor, MI, United States
    • University of Ioannina
      • Department of Chemistry
      Yannina, Epirus, Greece
  • 2008
    • French National Centre for Scientific Research
      • Institute for Molecular and Cellular Biology (IBMC)
      Paris, Ile-de-France, France
  • 2006–2007
    • It-Robotics
      Vicenza, Veneto, Italy
  • 2005
    • University of Zaragoza
      • Department of Organic Chemistry
      Caesaraugusta, Aragon, Spain
  • 2003–2004
    • Leiden University
      Leyden, South Holland, Netherlands
    • Lodz University of Technology
      • Institute of Organic Chemistry
      Łódź, Lodz Voivodeship, Poland
  • 2002
    • Istituto di Ricerche Chimiche e Biochimiche G. Ronzoni
      Milano, Lombardy, Italy
    • University of Ferrara
      Ferrare, Emilia-Romagna, Italy
    • University of Bologna
      • "Giacomo Ciamician" Department of Chemistry CHIM
      Bologna, Emilia-Romagna, Italy
  • 2000–2001
    • McMaster University
      • Department of Chemistry and Chemical Biology
      Hamilton, Ontario, Canada
  • 1994–2001
    • University of Naples Federico II
      • Department of Chemical, Materials and Industrial Production Engineering
      Napoli, Campania, Italy
  • 1999
    • Massachusetts Institute of Technology
      • Department of Chemistry
      Cambridge, MA, United States
  • 1996
    • Osaka University of Pharmaceutical Sciences
      Ōsaka, Ōsaka, Japan