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Casanovas J, Revilla-López G, Crisma M, Toniolo C, Alemán C. Factors Governing the Conformational Tendencies of Cα-Ethylated α-Amino Acids: Chirality and Side-Chain Size Effects. J Phys Chem B 2012; 116:13297-307. [DOI: 10.1021/jp3045115] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Moretto A, Crisma M, Formaggio F, Toniolo C. Peptide-based rotaxanes and catenanes: an emerging class of supramolecular chemistry systems. Biomol Concepts 2012; 3:183-92. [PMID: 25436531 DOI: 10.1515/bmc-2011-0061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Accepted: 01/02/2012] [Indexed: 11/15/2022] Open
Abstract
Abstract [2]Rotaxanes are interlocked molecular systems in which the cavity of a macrocycle (wheel) is threaded by a linear compound (axle). The axle is held in place principally by a sterically demanding moiety (stopper) at each end. If the two ends of a rotaxane are covalently linked together, then an assembly of two intertwined macrocycles (termed [2]catenane) is generated. Although rotaxanes and catenanes have been extensively investigated by several research groups, only a limited amount of studies has been devoted to these systems when a peptide molecule characterizes either the axle or the wheel(s) (or both). The purpose of this short conceptual overview is to summarize recent findings on synthetic and naturally occurring peptide-based [2]rotaxanes, [3]rotaxanes, and [2]catenanes and discuss future prospects for the research in this emerging area of supramolecular chemistry.
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Fabris F, De Lucchi O, Nardini I, Crisma M, Mazzanti A, Mason SA, Lemée-Cailleau MH, Scaramuzzo FA, Zonta C. (+)-syn-Benzotriborneol an enantiopure C3-symmetric receptor for water. Org Biomol Chem 2012; 10:2464-9. [PMID: 22349254 DOI: 10.1039/c2ob06774a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
(+)-syn-Benzotriborneol forms stable complexes with one molecule of water. This is due to the ability of the host to form three hydrogen bonds with water, to act simultaneously as a hydrogen-bond acceptor and donor, and to a perfect geometrical match between the pair. We report experimental (X-ray and neutron diffraction, VT NMR, DSC, TGA) and stereochemical studies carried out to elucidate and quantify the molecular and thermodynamic aspects of this supramolecular complex.
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Formaggio F, Crisma M, Ballano G, Peggion C, Venanzi M, Toniolo C. Novel peptide foldameric motifs: a step forward in our understanding of the fully-extended conformation/310-helix coexistence. Org Biomol Chem 2012; 10:2413-21. [DOI: 10.1039/c2ob06863j] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Formaggio F, Crisma M, Peggion C, Moretto A, Venanzi M, Toniolo C. Looking for a Robust, Synthetic, Fully-Extended (2.05-Helical) Peptide Structure - Effect of Terminal Groups. European J Org Chem 2011. [DOI: 10.1002/ejoc.201101273] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Carlotto S, Zerbetto M, Shabestari MH, Moretto A, Formaggio F, Crisma M, Toniolo C, Huber M, Polimeno A. In silico interpretation of cw-ESR at 9 and 95 GHz of mono- and bis- TOAC-labeled Aib-homopeptides in fluid and frozen acetonitrile. J Phys Chem B 2011; 115:13026-36. [PMID: 21970372 DOI: 10.1021/jp2063645] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this paper, we address the interpretation of molecular properties of selected singly and doubly spin-labeled peptides from continuous-wave electron spin resonance (cw-ESR) spectroscopy. This study is performed by means of an integrated computational approach that merges a stochastic treatment of long-term dynamics to ad hoc methodologies for the calculation of structural properties. In particular, our method is based on (i) the determination of geometric and local magnetic parameters of the peptides by quantum mechanical density functional calculations by taking into account solvent contribution; (ii) the hydrodynamic evaluation of dissipative properties; and (iii) molecular dynamics including equilibrium distribution of molecular conformations. The system is then described by a stochastic Liouville equation in which the spin Hamiltonian for the two electron spins, interacting with each other and coupled to two (14)N nuclear spins, is coupled to the diffusive operator describing the time evolution of slow coordinates. cw-ESR spectra are simulated for selected peptides built from the non-natural α-aminoacids α-aminoisobutyric acid (Aib) and 2,2,6,6-tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid (TOAC). In particular, we study the -Aib-TOAC-Aib- singly labeled tripeptide and the -Aib-TOAC-(Aib)(7)- singly labeled and -Aib-TOAC-(Aib)(5)-TOAC-Aib- doubly labeled nonapeptides. We show that good agreement is obtained with minimal resorting to fitting procedures, proving that the combination of sensitive ESR spectroscopy and sophisticated modeling is a powerful approach to the investigation of both molecular dynamics and 3D-structural properties.
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Fatás P, Longo E, Rastrelli F, Crisma M, Toniolo C, Jiménez AI, Cativiela C, Moretto A. Bis(azobenzene)-based photoswitchable, prochiral, Cα-tetrasubstituted α-amino acids for nanomaterials applications. Chemistry 2011; 17:12606-11. [PMID: 21956889 DOI: 10.1002/chem.201102609] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Indexed: 11/06/2022]
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De Zotti M, Biondi B, Crisma M, Hjørringgaard CU, Berg A, Brückner H, Toniolo C. Isovaline in naturally occurring peptides: A nondestructive methodology for configurational assignment. Biopolymers 2011; 98:36-49. [DOI: 10.1002/bip.21679] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2011] [Revised: 05/03/2011] [Accepted: 05/10/2011] [Indexed: 11/08/2022]
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Moretto A, Crisma M, Formaggio F, Toniolo C. Building a bridge between peptide chemistry and organic chemistry: intramolecular macrocyclization reactions and supramolecular chemistry with helical peptide substrates. Biopolymers 2011; 94:721-32. [PMID: 20564031 DOI: 10.1002/bip.21445] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In our ongoing efforts to build a bridge between peptide chemistry and organic chemistry, we are currently investigating: (1) two types of intramolecular macrocyclization reactions in 3(10)-helical peptides, and (2) a peptido[2]rotaxane molecular machine as a supramolecular tool using a 3(10)-helical peptide as the axle. More specifically, we studied the following two reactions: (a) the intramolecular ring-closing olefin metathesis between two amino acid residues with side chains bearing an allyl group, and (b) the intramolecular Paternò-Yang photoreaction, using a benzophenone-based amino acid as a photoaffinity reagent for a Met residue. Both reactions involve formation of a new C--C bond. As for the supramolecular system examined, we were able to identify the two stations of a new peptido[2]rotaxane characterized by an -(Aib)(6)- axle and to reversibly switch the aromatic tetramide macrocyclic wheel from one station to the next. This article summarizes the information available in the literature from other groups and the published/unpublished data originated from our laboratory on these research areas.
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Crisma M, Moretto A, Peggion C, Panella L, Kaptein B, Broxterman QB, Formaggio F, Toniolo C. Chiral, fully extended helical peptides. Amino Acids 2011; 41:629-41. [DOI: 10.1007/s00726-011-0839-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Accepted: 01/19/2011] [Indexed: 11/24/2022]
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Mba M, Moretto A, Armelao L, Crisma M, Toniolo C, Maggini M. Synthesis and self-assembly of oligo(p-phenylenevinylene) peptide conjugates in water. Chemistry 2011; 17:2044-7. [PMID: 21294174 DOI: 10.1002/chem.201002495] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2010] [Indexed: 11/09/2022]
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Gatto E, Caruso M, Porchetta A, Toniolo C, Formaggio F, Crisma M, Venanzi M. Photocurrent generation through peptide-based self-assembled monolayers on a gold surface: antenna and junction effects. J Pept Sci 2010; 17:124-31. [DOI: 10.1002/psc.1329] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Revised: 10/15/2010] [Accepted: 10/15/2010] [Indexed: 11/08/2022]
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Kamphuis J, Boesten WHJ, Schoemaker HE, Aubry A, Bayeul D, Dautant A, Pantano M, Formaggio F, Crisma M, Bonora GM, Toniolo C. Peptides from chiral Cα,α-disubstituted glycines. Synthesis and conformational analysis of homochiral (αMe) Leu / Ala model peptides. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19941130104] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Crisma M, Valle G, Pantano M, Formaggio F, Bonora GM, Toniolo C, Kamphuis J. Peptides from chiral Cαα-disubstituted glycines. On the helical screw sense of isovaline peptides. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19951140706] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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De Zotti M, Damato F, Formaggio F, Crisma M, Schievano E, Mammi S, Kaptein B, Broxterman QB, Felock PJ, Hazuda DJ, Singh SB, Kirschbaum J, Brückner H, Toniolo C. Total synthesis, characterization, and conformational analysis of the naturally occurring hexadecapeptide integramide A and a diastereomer. Chemistry 2010; 16:316-27. [PMID: 19937615 DOI: 10.1002/chem.200900945] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Integramide A is a 16-amino acid peptide inhibitor of the enzyme HIV-1 integrase. We have recently reported that the absolute stereochemistries of the dipeptide sequence near the C terminus are L-Iva(14)-D-Iva(15). Herein, we describe the syntheses of the natural compound and its D-Iva(14)-L-Iva(15) diastereomer, and the results of their chromatographic/mass spectrometric analyses. We present the conformational analysis of the two compounds and some of their synthetic intermediates of different main-chain length in the crystal state (by X-ray diffraction) and in solvents of different polarities (using circular dichroism, FTIR absorption, and 2D NMR techniques). These data shed light on the mechanism of inhibition of HIV-1 integrase, which is an important target for anti-HIV therapy.
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Wright K, Moretto A, Crisma M, Wakselman M, Mazaleyrat JP, Formaggio F, Toniolo C. A new tool for photoaffinity labeling studies: a partially constrained, benzophenone based, α-amino acid. Org Biomol Chem 2010; 8:3281-6. [DOI: 10.1039/c003943h] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Backus EHG, Bloem R, Pfister R, Moretto A, Crisma M, Toniolo C, Hamm P. Dynamical transition in a small helical peptide and its implication for vibrational energy transport. J Phys Chem B 2009; 113:13405-9. [PMID: 19754080 DOI: 10.1021/jp904905d] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The two-dimensional infrared spectrum of an octameric helical peptide in chloroform was measured as a function of temperature. Isotope labeling of the carbonyl group of one of the amino acids was used to obtain information for an isolated vibration. The antidiagonal width of the 2D-IR signal, which is a measure of the homogeneous dephasing time T(2), is constant from 220 to 260 K (within experimental error), and increases steeply above. The homogeneous dephasing time of the carbonyl vibration is attributed to the flexibility of the system and/or its immediate surrounding. The system undergoes a dynamical transition at about 270 K, with similarities to the protein dynamical transition. Furthermore, the temperature dependence of the antidiagonal width strongly resembles that of the efficiency of vibrational energy transport along the helix, which has been studied in a recent paper (J. Phys. Chem. B 2008, 112, 15487). The connection between the two processes, structural flexibility and energy transport mechanism, is discussed.
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Moretto A, Menegazzo I, Crisma M, Shotton E, Nowell H, Mammi S, Toniolo C. A Rigid Helical Peptide Axle for a [2]Rotaxane Molecular Machine. Angew Chem Int Ed Engl 2009; 48:8986-9. [DOI: 10.1002/anie.200904749] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Moretto A, Menegazzo I, Crisma M, Shotton E, Nowell H, Mammi S, Toniolo C. A Rigid Helical Peptide Axle for a [2]Rotaxane Molecular Machine. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200904749] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Schade M, Moretto A, Crisma M, Toniolo C, Hamm P. Vibrational Energy Transport in Peptide Helices after Excitation of C−D Modes in Leu-d10. J Phys Chem B 2009; 113:13393-7. [DOI: 10.1021/jp906363a] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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De Poli M, Moretto A, Crisma M, Peggion C, Formaggio F, Kaptein B, Broxterman QB, Toniolo C. Is the backbone conformation of C(alpha)-methyl proline restricted to a single region? Chemistry 2009; 15:8015-8025. [PMID: 19579242 DOI: 10.1002/chem.200900688] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
C(alpha)-methyl-L-proline, or L-(alphaMe)Pro, is probably the most conformationally constrained alpha-amino acid. In particular, its omega and phi torsion angles are restricted to about 180 and -60 degrees, respectively, and only three ranges of values are theoretically available for psi in mono- or longer peptides, namely, about -30 degrees (cis', 3(10)/alpha-helical structure), 60 degrees (inverse gamma turn), or 140 degrees (trans', poly(L-Pro)(n) II structure). In this work, we examined the tendency of a number of N(alpha)-acyl dipeptide N'-alkylamides of the type RCO-(alphaMe)Pro-Xxx-NHR' or RCO-Xxx-(alphaMe)Pro-NHR', in which Xxx is L (or D)-Ala, Aib (alpha-aminoisoburyric acid), or L (or D)-(alphaMe)Pro, long enough to fold into intramolecularly hydrogen-bonded gamma or beta turns. The results are compared with those obtained for the corresponding dipeptides based on Pro, a well-known turn-forming residue. For the crystal-state 3D-structural analysis we used X-ray diffraction, whereas our solution conformational analysis was heavily based on the FTIR absorption and (1)H and (13)C NMR spectroscopy techniques. We conclude that (alphaMe)Pro is able to explore both trans' and cis' psi areas of the conformational space, but in (alphaMe)Pro the latter is overwhelmingly more populated, in marked contrast to the Pro preference. This finding is a clear indication that in (alphaMe)Pro the major 3D-structural determinant is the C(alpha)-methyl group. The circular dichroism (CD) signature of a peptide type III' beta-turn conformation is also proposed.
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Geotti-Bianchini P, Crisma M, Peggion C, Bianco A, Formaggio F. Conformationally controlled, thymine-based alpha-nucleopeptides. Chem Commun (Camb) 2009:3178-80. [PMID: 19587905 DOI: 10.1039/b822789f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Rigid peptide backbones and backbone-to-side chain H-bonds permit the design of alpha-nucleopeptides with known 3D-structure; thymine-thymine base pairing is also observed.
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Moyo P, Guryanov I, Crisma M, Broxterman Q, Toniolo C, Decatur SM. Isotope-edited Infrared Spectroscopy of 3-10 Helical Peptides. Biophys J 2009. [DOI: 10.1016/j.bpj.2008.12.3050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Geotti-Bianchini P, Crisma M, Peggion C, Bianco A, Formaggio F. Synthesis and 3D-Structure of Conformationally Controlled Nucleo-Peptides. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2009; 611:37-8. [DOI: 10.1007/978-0-387-73657-0_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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