Fernando Formaggio

University of Padova, Padua, Veneto, Italy

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Publications (455)1267.26 Total impact

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    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) [6] 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) [7] 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).
    Full-text · Article · Mar 2016
  • M. Crisma · F. Formaggio · C. Toniolo
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    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.
    No preview · Article · Jan 2016
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    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
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    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
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    ABSTRACT: Pulsed EPR methods, in particular PELDOR (or DEER), are very sensitive to the dipole···dipole interaction between electron spins in a pair of free radicals. Using PELDOR, the conformations of a number of double radical-containing biomolecules have been determined. In this review article we focused our attention on the application of this spectroscopy to nitroxide-labeled peptaibols. This is an emerging class of naturally-occurring, relatively short, linear, helical peptide molecules endowed with hydrophobic character, capability to interact with and to alter the structure of membranes, and antibiotic activity. We extracted detailed information on the secondary structures of specifically site-directed, double nitroxide-labeled peptaibols under a variety of experimental conditions, including biologically relevant environments. Moreover, we examined in depth peptaibol clustering, related to the marked propensity of these molecules to undergo self-association in model and whole-cell membrane systems, using mainly mono nitroxide-containing synthetic analogs. Finally, based on the PELDOR data accumulated, we proposed models of supramolecular (quaternary) structures of peptaibols and their binding modes to membranes. This article is protected by copyright. All rights reserved. © 2015 Wiley Periodicals, Inc.
    No preview · Article · Aug 2015 · Biopolymers
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    ABSTRACT: Among the various types of α-peptide folding motifs, δ-turn, which requires a central cis-amide disposition, has been one of the least extensively investigated. In particular, this main-chain reversal topology has been studied in-depth neither in linear/cyclic peptides nor in proteins. This Minireview article assembles and critically analyzes relevant data from a literature survey on the δ-turn conformation in those compounds. Unpublished results from recent conformational energy calculations and a preliminary solution-state analysis on a small model peptide, currently ongoing in our laboratories, are also briefly outlined. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
    Preview · Article · Aug 2015 · Chemistry - A European Journal
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    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.
    Full-text · Article · Jul 2015 · Nanoscale
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    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.
    Full-text · Article · Jul 2015 · ChemistryOpen
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    ABSTRACT: Total syntheses and complete characterizations of singly substituted PheCN -based analogs of alamethicin AlaP, which is active on model and natural membranes, and the TM peptide, which inserts in a trans-membrane orientation in lipid bilayers, are reported. The syntheses of the AlaP analogs were performed in solution, while those of TM and its analogs were carried out by solid phase. Using the cyanophenyl fluorescence and IR absorption probe, an in-depth investigation of the self-association, membrane-interacting, permeabilizing, and orientation properties of these peptides were conducted. The aromatic residue incorporated induces only a negligible modification to the properties of the parent peptides. The PheCN IR absorption band was located between 2228-2230 cm(-1) for all peptides, irrespective of the position of labeling. By contrast, as the width of this band varied significantly with the depth of probe insertion in the bilayer, it could represent a good marker of the PheCN position in phospholipid membranes. This article is protected by copyright. All rights reserved. © 2015 Wiley Periodicals, Inc.
    No preview · Article · May 2015 · Biopolymers
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    ABSTRACT: Two analogs of the ten-amino acid residue, membrane-active lipopeptaibiotic trichogin GA IV, mono-labeled with 4-cyano-α-methyl-L-phenylalanine, a potentially useful fluorescence and IR absorption probe of the local microenvironment, were synthesized by the solid-phase methodology and conformationally characterized. The single modification was incorporated either at the N-terminus (position 1) or near the C-terminus (position 8) of the peptide main chain. In both cases, the replaced amino acid was the equally helicogenic α-aminoisobutyric acid (Aib) residue. We performed a solution conformational analysis by use of FT-IR absorption, CD, and 2D-NMR spectroscopies. The results indicate that both labeled analogs essentially maintain the overall helical propensity of the naturally occurring lipopeptaibiotic. Peptidemembrane interactions were assessed by fluorescence and ATR-IR absorption techniques. Analogies and differences between the two peptides were highlighted. Taken together, our data confirm literature results that some of the spectroscopic parameters of the 4-cyanobenzyl chromophore are sensitive markers of the local microenvironment. Copyright © 2015 Verlag Helvetica Chimica Acta AG, Zürich.
    No preview · Article · Apr 2015 · Chemistry & Biodiversity
  • Hiroaki Maekawa · Gema Ballano · Fernando Formaggio · Claudio Toniolo · Nien-Hui Ge
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    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
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    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
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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.
    Full-text · Article · Oct 2014 · Biochimica et Biophysica Acta (BBA) - Biomembranes
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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.
    No preview · Article · Aug 2014 · Chemistry & Biodiversity
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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.
    No preview · Article · Jul 2014 · Physical Chemistry Chemical Physics
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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.
    No preview · Article · Jul 2014 · Journal of Peptide Science
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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.
    Full-text · Article · Jul 2014 · Chemistry & Biodiversity
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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.
    No preview · Article · Jul 2014 · Journal of Peptide Science
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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.
    No preview · Article · Jun 2014 · The Journal of Physical Chemistry B
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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.
    Full-text · Article · Jun 2014 · The Journal of Physical Chemistry A

Publication Stats

8k Citations
1,267.26 Total Impact Points


  • 1986-2015
    • University of Padova
      • Department of Chemical Sciences
      Padua, Veneto, Italy
  • 2002-2009
    • University of Rome Tor Vergata
      • Dipartimento di Scienze e Tecnologie Chimiche
      Roma, Latium, Italy
  • 2000-2009
    • National Research Council
      • • Institute of Biomolecular Chemistry ICB
      • • Laboratory of Organic Chemistry
      Roma, Latium, Italy
    • McMaster University
      • Department of Chemistry and Chemical Biology
      Hamilton, Ontario, Canada
  • 2007
    • Leiden University
      Leyden, South Holland, Netherlands
  • 2006-2007
    • It-Robotics
      Vicenza, Veneto, Italy
  • 1998
    • Lodz University of Technology
      • Institute of Organic Chemistry
      Łódź, Łódź Voivodeship, Poland
  • 1994-1997
    • University of Naples Federico II
      • Department of Chemical, Materials and Industrial Production Engineering
      Napoli, Campania, Italy
  • 1995
    • Osaka University of Pharmaceutical Sciences
      Ōsaka, Ōsaka, Japan
    • University of Illinois at Chicago
      • Department of Chemistry
      Chicago, Illinois, United States