501
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Mazaleyrat JP, Wright K, Gaucher A, Toulemonde N, Dutot L, Wakselman M, Broxterman QB, Kaptein B, Oancea S, Peggion C, Crisma M, Formaggio F, Toniolo C. Induced Axial Chirality in the Biphenyl Core of the Proatropoisomeric, Cα-Tetrasubstituted α-Amino Acid Residue Bip in Peptides. Chemistry 2005; 11:6921-9. [PMID: 16021648 DOI: 10.1002/chem.200500187] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
An induced axial chirality in the biphenyl core of the 2',1':1,2;1'',2'':3,4-dibenzcyclohepta-1,3-diene-6-amino-6-carboxylic acid (Bip) residue, a conformationally labile, atropoisomeric, C(alpha)-tetrasubstituted alpha-amino acid, was observed by CD and (1)H NMR spectroscopic techniques in the linear dipeptides Boc-Bip-Xaa*-OMe where Boc=tert-butoxycarbonyl, OMe=methoxy, and Xaa*=D- and/or L-Ala, -Val, -Leu, -Phe, -(alphaMe)Val and -(alphaMe)Leu. Chiral induction was significantly lower in the isomeric dipeptides Boc-Xaa*-Bip-OMe, with the Xaa* residue located at the N-terminus of Bip, as well as in the cyclic dipeptide cyclo-[Bip-L-Ala]. The results obtained in solution were confirmed by X-ray diffraction analysis of a crystalline sample of Boc-(R)-Bip-D-Ala-OMe.
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502
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Saro D, Klosi E, Paredes A, Spaller MR. Thermodynamic analysis of a hydrophobic binding site: probing the PDZ domain with nonproteinogenic peptide ligands. Org Lett 2005; 6:3429-32. [PMID: 15387515 DOI: 10.1021/ol049181q] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[structure: see text] Isothermal titration calorimetry (ITC) is used to study the thermodynamic consequences of systematically modifying the hydrophobic character of a single residue in a series of protein-binding ligands. By substituting standard and nonproteinogenic aliphatic amino acids for the C-terminal valine of the hexapeptide KKETEV, binding to the third PDZ domain (PDZ3) of the PSD-95 protein is characterized by distinct changes in the Gibbs free energy (DeltaG), enthalpy (DeltaH), and entropy (TDeltaS) parameters. One notable observation is that peptide binding affinity can be improved with a nonstandard residue.
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Affiliation(s)
- Dorina Saro
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
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503
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Crisma M, Deschamps JR, George C, Flippen-Anderson JL, Kaptein B, Broxterman QB, Moretto A, Oancea S, Jost M, Formaggio F, Toniolo C. A topographically and conformationally constrained, spin-labeled, alpha-amino acid: crystallographic characterization in peptides. ACTA ACUST UNITED AC 2005; 65:564-79. [PMID: 15885116 DOI: 10.1111/j.1399-3011.2005.00258.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
2,2,6,6-Tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid (TOAC) is a topographically and conformationally restricted, nitroxide containing, C(alpha)-tetrasubstituted alpha-amino acid. Here, we describe the molecular and crystal structures, as determined by X-ray diffraction analyses, of a TOAC terminally protected derivative, the cyclic dipeptide c(TOAC)(2).1,1,1,3,3,3-hexafluoropropan-2-ol (HFIP) solvate, and five TOAC-containing, terminally protected, linear peptides ranging in length from tetra- to hepta-peptides. Incipient and fully developed, regular or distorted 3(10)-helical structures are formed by the linear peptides. A detailed discussion on the average geometry and preferred conformation for the TOAC piperidine ring is also reported. The X-ray diffraction structure of an intramolecularly cyclized side product resulting from a C-activated TOAC residue has also been determined.
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Affiliation(s)
- M Crisma
- Department of Chemistry, Institute of Biomolecular Chemistry, CNR, University of Padova, 35131 Padova, Italy
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504
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Jiménez AI, López P, Cativiela C. Synthesis and HPLC enantioseparation of the cyclopropane analogue of valine (c3Val). Chirality 2005; 17:22-9. [PMID: 15515045 DOI: 10.1002/chir.20091] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A new and efficient method is presented for the preparation of the N-Boc-protected cyclopropane analogue of valine, 1-(N-tert-butoxycarbonyl)amino-2,2-dimethylcyclopropanecarboxylic acid, both in racemic and enantiomerically pure forms. Cyclopropanation of the exocyclic double bond of 2-phenyl-4-isopropylidene-5(4H)-oxazolone with diazomethane followed by elaboration of the heterocyclic moiety provided multigram quantities of the racemic target compound. Subsequent HPLC resolution of a racemic precursor on a noncommercial chiral stationary phase has given access to enantiomerically pure products. Almost 1.5 g of the first-eluted enantiomer and 1.0 g of the second-eluted enantiomer have been isolated in optically pure form using a 150 x 20 mm ID column containing mixed 10-undecenoate/3,5-dimethylphenylcarbamate of cellulose covalently bonded to allylsilica gel with a mixture of hexanes/tert-butyl methyl ether/ethyl acetate as the mobile phase.
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Affiliation(s)
- Ana I Jiménez
- Departamento de Química Orgánica, ICMA, Universidad de Zaragoza-CSIC, Zaragoza, Spain
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505
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Zelezetsky I, Pacor S, Pag U, Papo N, Shai Y, Sahl HG, Tossi A. Controlled alteration of the shape and conformational stability of alpha-helical cell-lytic peptides: effect on mode of action and cell specificity. Biochem J 2005; 390:177-88. [PMID: 15836439 PMCID: PMC1184573 DOI: 10.1042/bj20042138] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2004] [Revised: 04/05/2005] [Accepted: 04/19/2005] [Indexed: 11/17/2022]
Abstract
A novel method, based on the rational and systematic modulation of macroscopic structural characteristics on a template originating from a large number of natural, cell-lytic, amphipathic alpha-helical peptides, was used to probe how the depths and shapes of hydrophobic and polar faces and the conformational stability affect antimicrobial activity and selectivity with respect to eukaryotic cells. A plausible mode of action explaining the peptides' behaviour in model membranes, bacteria and host cells is proposed. Cytotoxic activity, in general, correlated strongly with the hydrophobic sector depth, and required a majority of aliphatic residue side chains having more than two carbon atoms. It also correlated significantly with the size of polar sector residues, which determines the penetration depth of the peptide via the so-called snorkel effect. Both an oblique gradient of long to short aliphatic residues along the hydrophobic face and a stabilized helical structure increased activity against host cells but not against bacteria, as revealed by haemolysis, flow cytofluorimetric studies on lymphocytes and surface plasmon resonance studies with model phosphatidylcholine/cholesterol membranes. The mode of interaction changes radically for a peptide with a stable, preformed helical conformation compared with others that form a structure only on membrane binding. The close correlation between effects observed in biological and model systems suggests that the 'carpet model' correctly represents the type of peptides that are bacteria-selective, whereas the behaviour of those that lyse host cells is more complex.
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Key Words
- amphipathic helix
- antimicrobial peptide
- cell specificity
- cell-lytic peptide
- mode of action
- surface plasmon resonance
- abu, 2-aminobutyric acid
- acp, aminocylcopentanecarboxylic acid
- aib, 2-aminoisobutyric acid
- amp, antimicrobial peptide
- dab, 2,4-diaminobutyric acid
- dap, 2,3-diaminopropionic acid
- deg, diethylglycine
- dpg, dipropylglycine
- fs, forward scattering
- hse, homoserine
- mh, mueller–hinton
- mic, minimum inhibitory concentration
- nle, norleucine
- nva, norvaline
- onpg, o-nitrophenyl β-d-galactopyranoside
- pc, phosphatidylcholine
- pe, phosphatidylethanolamine
- pg, phosphatidylglycerol
- pi, propidium iodide
- sem, scanning electron microscopy
- spr, surface plasmon resonance
- ss, side scattering
- tfe, trifluoroethanol
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Affiliation(s)
- Igor Zelezetsky
- *Department of Biochemistry, Biophysics and Macromolecular Chemistry, University of Trieste, I-34127 Trieste, Italy
| | - Sabrina Pacor
- †Department of Biomedical Sciences, University of Trieste, I-34127 Trieste, Italy
| | - Ulrike Pag
- ‡Institute for Medical Microbiology and Immunology, University of Bonn, 53105 Bonn, Germany
| | - Niv Papo
- §Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yechiel Shai
- §Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Hans-Georg Sahl
- ‡Institute for Medical Microbiology and Immunology, University of Bonn, 53105 Bonn, Germany
| | - Alessandro Tossi
- *Department of Biochemistry, Biophysics and Macromolecular Chemistry, University of Trieste, I-34127 Trieste, Italy
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506
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Sartori E, Corvaja C, Oancea S, Formaggio F, Crisma M, Toniolo C. Linear Configuration of the Spins of a Stable Trinitroxide Radical Based on a Ternary Helical Peptide. Chemphyschem 2005; 6:1472-5. [PMID: 15999386 DOI: 10.1002/cphc.200500139] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Elena Sartori
- Department of Chemistry, University of Padova, via Marzolo, 1, 35131 Padova, Italy
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507
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Cativiela C, Lasa M, López P. Synthesis of enantiomerically pure cis- and trans-cyclopentane analogues of phenylalanine. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/j.tetasy.2005.06.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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508
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Barazza A, Wittelsberger A, Fiori N, Schievano E, Mammi S, Toniolo C, Alexander JM, Rosenblatt M, Peggion E, Chorev M. Bioactive N-terminal undecapeptides derived from parathyroid hormone: the role of alpha-helicity. ACTA ACUST UNITED AC 2005; 65:23-35. [PMID: 15686531 DOI: 10.1111/j.1399-3011.2005.00207.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The N-terminal 1-34 segment of parathyroid hormone (PTH) is fully active in vitro and in vivo and it can reproduce all biological responses in bone characteristic of the native intact PTH. Recent studies have demonstrated that N-terminal fragments presenting the principal activating domain such as PTH(1-11) and PTH(1-14) with helicity-enhancing substitutions yield potent analogues with PTH(1-34)-like activity. To further investigate the role of alpha-helicity on biological potency, we designed and synthesized by solid-phase methodology the following hPTH(1-11) analogues substituted at positions 1 and/or 3 by the sterically hindered and helix-promoting C(alpha)-tetrasubstituted alpha-amino acids alpha-amino isobutyric acid (Aib), 1-aminocyclopentane-1-carboxylic acid (Ac(5)c) and 1-aminocyclohexane-1-carboxylic acid (Ac(6)c): Ac(5)c-V-Aib-E-I-Q-L-M-H-Q-R-NH(2) (I); Aib-V-Ac(5)c-E-I-Q-L-M-H-Q-R-NH(2) (II); Ac(6)c-V-Aib-E-I-Q-L-M-H-Q-R-NH(2) (III); Aib-V-Ac(6)c-E-I-Q-L-M-H-Q-R-NH(2) (IV); Aib-V-Aib-E-I-Q-L-M-H-Q-R-NH(2) (V); S-V-Aib-E-I-Q-L-M-H-Q-R-NH(2) (VI), S-V-Ac(5)c-E-I-Q-L-M-H-Q-R-NH(2) (VII); Ac(5)c-V-S-E-I-Q-L-M-H-Q-R-NH(2) (VIII); Ac(6)c-V-S-E-I-Q-L-M-H-Q-R-NH(2) (IX); Ac(5)c-V-Ac(5)c-E-I-Q-L-M-H-Q-R-NH(2) (X); Ac(6)c-V-Ac(6)c-E-I-Q-L-M-H-Q-R-NH(2) (XI). All analogues were biologically evaluated and conformationally characterized in 2,2,2-trifluoroethanol (TFE) solution by circular dichroism (CD). Analogues I-V, which cover the full range of biological activity observed in the present study, were further conformationally characterized in detail by nuclear magnetic resonance (NMR) and computer simulations studies. The results of ligand-stimulated cAMP accumulation experiments indicated that analogues I and II are active, analogues III, VI and VII are very weakly active and analogues IV, V, VIII-XI are inactive. The most potent analogue, I exhibits biological activity 3500-fold higher than that of the native PTH(1-11) and only 15-fold weaker than that of the native sequence hPTH(1-34). Remarkably, the two most potent analogues, I and II, and the very weakly active analogues, VI and VII, exhibit similar helix contents. These results indicate that the presence of a stable N-terminal helical sequence is an important but not sufficient condition for biological activity.
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Affiliation(s)
- A Barazza
- Division of Bone and Mineral Research, Beth Israel Deaconess Medical Center and Harvard Medical School, 330 Brookline Ave, Boston, MA 02215, USA
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509
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Naider F, Khare S, Arshava B, Severino B, Russo J, Becker JM. Synthetic peptides as probes for conformational preferences of domains of membrane receptors. Biopolymers 2005; 80:199-213. [PMID: 15622547 DOI: 10.1002/bip.20183] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Peptide models have been widely used to investigate conformational aspects of domains of proteins since the early 1950s. A pioneer in this field was Dr. Murray Goodman, who applied a battery of methodologies to study the onset of structure in homooligopeptides. This article reviews some of Dr. Goodman's contributions, and reports recent studies using linear and constrained peptides corresponding to the first extracellular loop and linear peptides corresponding to the sixth transmembrane domain of a G-protein coupled receptor from the yeast Saccharomyces cerevisiae. Peptides containing 30-40 residues were synthesized using solid-phase methods and purified to near homogeneity by reversed phase high performance liquid chromatography. CD and NMR analyses indicated that the first extracellular loop peptides were mostly flexible in water, and assumed some helical structure near the N-terminus in trifluoroethanol and in the presence of micelles. Comparison of oligolysines with native loop residues revealed that three lysines at each terminus of a peptide corresponding to the sixth transmembrane domain of the alpha-factor receptor resulted in better aqueous solubility and greater helicity than the native loop residues.
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Affiliation(s)
- Fred Naider
- Department of Chemistry, College of Staten Island, and Institute for Macromolecular Assemblies, City University of New York, Staten Island, NY 10314, USA.
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510
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Schievano E, Pagano K, Mammi S, Peggion E. Conformational studies of Aib-rich peptides containing lactam-bridged side chains: evidence of 3(10)-helix formation. Biopolymers 2005; 80:294-302. [PMID: 15633206 DOI: 10.1002/bip.20199] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Aib-rich side-chain lactam-bridged oligomers Ac-(Glu-Aib-Aib-Lys)n-Ala-OH with n = 1,2,3 were designed and synthesized as putative models of the 3(10)-helix. The lactam bridge between the side chains of L-Glu and L-Lys in (i)--(i + 3) positions was introduced in order to enhance the structural preference toward the right-handed 3(10)-helix. The conformational properties of the three peptides were studied in trifluoroethanol (TFE) solution by CD, NMR, and computer simulations. The structural information was derived mainly from the analysis of nuclear Overhauser effect spectroscopy spectra. The presence of alpha H(i)-HN(i + 2) and of alpha H(i)-HN(i + 3) connectivities and the absence of alpha H(i)-HN(i + 4) connectivities indicate that these peptides fold into a 3(10)-helix rather than into an alpha-helix. Based on these conformational features, stereospecific assignment of the Aib methyl groups was possible. The results of such experiments and of the subsequent distance geometry and restrained molecular dynamics simulations reveal a marked preference of these peptides for 3(10)-helix. The CD spectra of these peptides indicate that the helix content increases upon chain elongation. The CD spectrum of the trimer is characterized by a negative band at 200 nm and by a weak positive band around 220 nm. The CD spectrum in TFE is different from that observed in aqueous solution in the presence of SDS micelles, reported in our previous work, and from those reported by a different research group for 3(10)-helical peptides. A possible reason for these differences could rest in the presence of different equilibria of the conformer populations of the various peptides in different solvent systems.
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Affiliation(s)
- E Schievano
- Department of Chemistry, University of Padova, Institute of Biomolecular Chemistry, CNR, Via Marzolo 1, 35131 Padova, Italy
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511
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Venanzi M, Valeri A, Palleschi A, Stella L, Moroder L, Formaggio F, Toniolo C, Pispisa B. Structural properties and photophysical behavior of conformationally constrained hexapeptides functionalized with a new fluorescent analog of tryptophan and a nitroxide radical quencher. Biopolymers 2005; 75:128-39. [PMID: 15356867 DOI: 10.1002/bip.20110] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The influence of the conformational properties on the photophysics of two de novo designed hexapeptides was studied by spectroscopic measurements (ir, NMR, steady-state, and time resolved fluorescence) and molecular mechanics calculations. The peptide sequences comprise two nonproteinogenic residues: a beta-(1-azulenyl)-L-alanine (Aal) residue, obtained by formally functionalizing the Ala side chain with the azulene chromophore, and a Calpha-tetrasubstituted alpha-amino acid (TOAC), incorporating a nitroxide group in a cycloalkyl moiety. Aal represents a new fluorescent, quasi-isosteric Trp analog and TOAC a stable radical species, frequently used as a paramagnetic probe in biochemical studies. The peptide chains differ in the sequence position of the two probes and are heavily based on Aib (alpha-aminoisobutyric acid) residues to generate conformationally restricted helical structures, as confirmed by both spectroscopic and computational results. The conformationally controlled, excited state interactions, determining the photophysical relaxation of the Aal*/TOAC pair, are also discussed.
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Affiliation(s)
- Mariano Venanzi
- Department of Chemical Sciences and Technologies, University of Tor Vergata, 00133 Rome, Italy.
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512
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Morera E, Nalli M, Mollica A, Paglialunga Paradisi M, Aschi M, Gavuzzo E, Mazza F, Lucente G. Peptides containing 4-amino-1,2-dithiolane-4-carboxylic acid (Adt): conformation of Boc-Adt-Adt-NHMe and NH...S interactions. J Pept Sci 2005; 11:104-12. [PMID: 15635640 DOI: 10.1002/psc.602] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
To study the conformational preferences induced by the insertion of the 4-amino-1,2-dithiolane-4-carboxylic acid (Adt) residue into a peptide backbone, the achiral N-protected dipeptide methylamide Boc-Adt-Adt-NHMe (1) was synthesized and its crystal state and solution conformation studied and compared with that exhibited by its carba-analogue Boc-Ac5c-Ac5c-NHMe containing two residues of 1-aminocyclopentane-1-carboxylic acid (Ac5c). Compound 1 in the crystal adopts a type-III beta-turn conformation and an analogous structure is that preferred in chloroform solution as established by 1H-NMR and NOE information. In the crystal packing three different Adt rings form a cavity and the involved sulphur atoms give rise to unusual multiple interactions with one NH group. The chemical nature of these intermolecular and intramolecular main-chain...side-chain NH...S interactions are discussed in terms of quantum chemical calculations.
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Affiliation(s)
- Enrico Morera
- Dipartimento di Studi Farmaceutici, Università di Roma La Sapienza and Istituto di Chimica Biomolecolare, Sezione di Roma, CNR, 00185 Roma, Italy
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513
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Kubasik M, Blom A. Acceleration of Short Helical Peptide Conformational Dynamics by Trifluoroethanol in an Organic Solvent. Chembiochem 2005; 6:1187-90. [PMID: 15937985 DOI: 10.1002/cbic.200400198] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Matthew Kubasik
- Department of Chemistry, Fairfield University, Fairfield, CT 06824, USA.
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514
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Singh Rathore R. Crystal structure and conformational analyses of a synthetic tetrapeptide t-Boc-L-Val-Aib-Gly-L-Leu-OMe. CRYSTAL RESEARCH AND TECHNOLOGY 2005. [DOI: 10.1002/crat.200410394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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515
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Das AK, Banerjee A, Drew MG, Ray S, Haldar D, Banerjee A. Can a consecutive double turn conformation be considered as a peptide based molecular scaffold for supramolecular helix in the solid state? Tetrahedron 2005. [DOI: 10.1016/j.tet.2005.03.057] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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516
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Royo S, De Borggraeve WM, Peggion C, Formaggio F, Crisma M, Jiménez AI, Cativiela C, Toniolo C. Turn and helical peptide handedness governed exclusively by side-chain chiral centers. J Am Chem Soc 2005; 127:2036-7. [PMID: 15713068 DOI: 10.1021/ja043116u] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have examined the preferred 3D structure of homopeptides based on an alpha-amino acid lacking the asymmetry at the alpha-carbon but exhibiting chirality in the side chains (at the two beta-carbons). These joint stereochemical properties are remarkably unusual for an alpha-amino acid. To this end, we carried out an experimental investigation by X-ray diffraction and NMR spectrometry. The results point to a well-defined relationship between screw sense of the turn and helix structures formed and side-chain configurations.
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Affiliation(s)
- Soledad Royo
- Department of Organic Chemistry, ICMA, University of Zaragoza-CSIC, 50009 Zaragoza, Spain
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517
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Formaggio F, Baldini C, Moretto V, Crisma M, Kaptein B, Broxterman QB, Toniolo C. Preferred Conformations of Peptides Containingtert-Leucine, a Sterically Demanding, Lipophilic ?-Amino Acid with a Quaternary Side-Chain C? Atom. Chemistry 2005; 11:2395-404. [PMID: 15669065 DOI: 10.1002/chem.200400892] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Terminally protected homopeptides of tert-leucine, from the dimer to the hexamer, co-oligopeptides of tert-leucine in combination with alpha-aminoisobutyric acid or glycine residues up to the hexamer level, and simple dipeptides representing known scaffolds for catalysts in asymmetric organic reactions were prepared by solution methods and fully characterized. The results of conformation analysis, performed by use of FT-IR absorption, NMR, CD, and X-ray diffraction techniques, indicate that this hydrophobic alpha-amino acid with tetrasubstitution at the Cbeta atom is structurally versatile. We show that it prefers extended or semiextended conformations, but can also be accommodated in folded structures, provided that these are biased by the presence of helicogenic residues. The current large-scale production of Tle, combined with its conformational preferences unravelled in this work, should make this bulky, hydrophobic, Calpha-trisubstituted alpha-amino acid a regular building block of any strategy seeking to tailor peptides with improved catalytic and pharmacological properties.
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Affiliation(s)
- Fernando Formaggio
- Institute of Biomolecular Chemistry, CNR, and Department of Chemistry, University of Padova, via Marzolo 1, 35131 Padova, Italy.
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518
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Toniolo C, Crisma M, Formaggio F, Peggion C, Broxterman Q, Kaptein B. Peptide β-Bend and 3 10-Helix: from 3D-Structural Studies to Applications as Templates. ACTA ACUST UNITED AC 2005. [DOI: 10.1007/s10847-004-0912-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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519
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Setnicka V, Huang R, Thomas CL, Etienne MA, Kubelka J, Hammer RP, Keiderling TA. IR Study of Cross-Strand Coupling in a β-Hairpin Peptide Using Isotopic Labels. J Am Chem Soc 2005; 127:4992-3. [PMID: 15810813 DOI: 10.1021/ja043007f] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Model beta-hairpin peptides can be used to develop understanding of fundamental elements of beta-sheet secondary structure formation and stability. We have studied two 13C-labeled variants of a beta-hairpin peptide modified from a design originally proposed by Gellman: Arg-Tyr-Val-Glu-Val-Aib-Gly-Lys-Lys-Ile-Leu-Gln. (In this peptide, the two italicized residues form a beta-turn, while 13C-labels are on the amide C=O of Val3, Lys8 in HBG-L and Val3, Ile10 in HBG-S.) Both these peptides are labeled on opposite strands of the hairpin, but differ in the labeling pattern. One (HBG-L) forms a large (14-atom) H-bonded ring of labeled C=Os, while the other (HBG-S) forms a small (10-atom) H-bonded ring. These impact the amide I infrared spectra, with HBG-L having a 13C frequency and intensity higher than that of HBG-S, in good agreement with our spectral simulations based on quantum mechanically derived force fields. The thermal behavior of both peptides yields a broad thermal transition and lacks an isosbestic point. The 13C band for HBG-L has the largest intensity change with temperature, distinct from the 12C change and the HBG-S 13C change.
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Affiliation(s)
- Vladimír Setnicka
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607-7061, USA
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520
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Licini G, Prins LJ, Scrimin P. Oligopeptide Foldamers: From Structure to Function. European J Org Chem 2005. [DOI: 10.1002/ejoc.200400521] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Giulia Licini
- University of Padova, Department of Chemical Sciences, and ITM‐CNR, Padova Section, Via Marzolo, 1, 35131 Padova, Italy
| | - Leonard J. Prins
- University of Padova, Department of Chemical Sciences, and ITM‐CNR, Padova Section, Via Marzolo, 1, 35131 Padova, Italy
| | - Paolo Scrimin
- University of Padova, Department of Chemical Sciences, and ITM‐CNR, Padova Section, Via Marzolo, 1, 35131 Padova, Italy
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521
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Toniolo C. From coded to non-coded alpha-amino acids: a journey in oligopeptide stereochemistry. J Pept Sci 2005; 11:250-3. [PMID: 15700235 DOI: 10.1002/psc.648] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Claudio Toniolo
- Institute of Biomolecular Chemistry, CNR, Department of Chemistry, University of Padova, 35131 Padova, Italy.
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522
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Becucci L, Guidelli R, Peggion C, Toniolo C, Moncelli MR. Incorporation of channel-forming peptides in a Hg-supported lipid bilayer. J Electroanal Chem (Lausanne) 2005. [DOI: 10.1016/j.jelechem.2004.09.032] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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523
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Peggion C, Coin I, Toniolo C. Total synthesis in solution of alamethicin F50/5 by an easily tunable segment condensation approach. Biopolymers 2005; 76:485-93. [PMID: 15499566 DOI: 10.1002/bip.20161] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A total synthesis in solution of the 19-mer peptide component F50/5 of alamethicin, the most extensively investigated among the channel-former peptaibol antibiotics, is reported. Three peptide segments (A, B, C) were prepared and assembled, followed by incorporation of the acetylated N-terminal amino acid. The synthetic modules B and C are characterized by three Glu(OMe) residues (at positions 7, 18, and 19) that, after completion of the synthesis, were reacted with ammonia to provide alamethicin F50/5. By use of this general strategy, we also prepared the [Gln7, Glu(OMe)18,19] alamethicin F50/5 analogue. The purity and conformation of the final products were assessed by chromatographic, spectrometric, and spectroscopic techniques. This tunable segment condensation approach will pave the way for an easy synthesis of alamethicin analogues bearing amino acid residues with desired side-chain probes even at the N-terminus and in internal positions of the sequence.
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Affiliation(s)
- Cristina Peggion
- Department of Chemistry, University of Padova, 35131 Padova, Italy
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524
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Raap J, Erkelens K, Ogrel A, Skladnev DA, Brückner H. Fungal biosynthesis of non-ribosomal peptide antibiotics and α, α-dialkylated amino acid constituents. J Pept Sci 2005; 11:331-8. [PMID: 15635654 DOI: 10.1002/psc.621] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Zervamicins (Zrv) IIA and IIB are membrane modifying peptide antibiotics of fungal origin, characterized by a sequence of 15 amino acid residues. The primary structure of Zrv-IIA contains five alpha-aminoisobutyric acid residues at positions 4, 7, 9, 12 and 14 of the linear peptide. The sequence of Zrv-IIB is similar, but contains a D-isovaline at position 4. When the free amino acid Aib was added to the peptone-glucose culture medium, the fungus Emericellopsis salmosynnemata produced Zrv-IIA as the major secondary metabolite, whereas addition of DL-Iva to the culture led to a high production of Zrv-IIB. This observation is rationalized by a lack of selectivity of the non-ribosomal peptide synthetase with respect to the thiolester activated amino acid substrates during step 12 of peptide synthesis. Analysis of the configuration of the Iva residue of Zrv-IIB showed a high enantiomeric purity of the D-enantiomer, indicating a high stereoselectivity of the peptide synthetase for this substrate.When the culture was supplemented with [(15)N]DL-Iva, the nitrogen isotope was not only found at the D-Iva residue, but surprisingly also at the Aib residues as well as at the proteinogenic residues of Zrv. The partial catabolism of exogenous [(15)N]DL-Iva is explained by the assumption of a decarboxylation-dependent transamination reaction, catalysed by 2,2-dimethylglycine decarboxylase. The same enzyme might also be involved in the reversed carboxylation reactions of acetone and 2-butanone, during the anabolic biosynthesis of Aib and Iva, respectively. Zrv might possibly act as a thermodynamic sink to shift these equilibrium reactions towards the reversed side.
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Affiliation(s)
- Jan Raap
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Leiden, The Netherlands.
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525
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Moretto A, Peggion C, Formaggio F, Crisma M, Kaptein B, Broxterman QB, Toniolo C. Stereoselective acylation of a racemic amine with Cα-methyl phenylglycine-based dipeptide 5(4H)-oxazolones. Chirality 2005; 17:481-7. [PMID: 16113993 DOI: 10.1002/chir.20182] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Reactions of a racemic amine with chiral, N(alpha)-acetylated, C(alpha)-methyl l-phenylglycine-based dipeptide 5(4H)-oxazolones proceed diastereoselectively to give predominantly dipeptide alkylamides comprising d-alpha-phenylethylamine. Diastereoselectivity is remarkably sensitive to solvent polarity and reaction temperature but not significantly to the nature of the C(alpha)-tetrasubstituted alpha-amino acid at position 1 of the dipeptide. The beta-turn 3D structures of the aminolysis products were established in CDCl(3) solution by FT-IR absorption and in one case in the crystal state by X-ray diffraction as well.
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Affiliation(s)
- Alessandro Moretto
- Institute of Biomolecular Chemistry, CNR, Department of Chemistry, University of Padova, Padova, Italy
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526
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Milov AD, Erilov DA, Salnikov ES, Tsvetkov YD, Formaggio F, Toniolo C, Raap J. Structure and spatial distribution of the spin-labelled lipopeptide trichogin GA IV in a phospholipid membrane studied by pulsed electron–electron double resonance (PELDOR). Phys Chem Chem Phys 2005; 7:1794-9. [DOI: 10.1039/b418414a] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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527
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Rathore RS. Conformational investigations on analogs of inflammation response inducing chemotactic tripeptide fMLP. Biopolymers 2005; 80:651-64. [PMID: 15648091 DOI: 10.1002/bip.20231] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Conformations of three analogs of for-L-Met-L-Leu-L-Phe-OH (fMLP), which initiates inflammatory response by interaction with the formyl peptide receptor (FPR), have been investigated by the application of the X-ray crystallographic technique. The investigated analogs of fMLP peptides are as follows: for-L-Met-1-amino-1-cyclooctane-carbonyl(Ac8c)-L-Phe-OMe; for-L-Met-L-Leu-L-p-iodo-Phe-OH; and for-L-Met-di-n-propylglycyl(Dpg)-L-Phe-OMe. The peptide backbone in and is constrained at position of fMLP by the introduction of Calpha,alpha-disubstituted glycines. In peptide, Phe-OMe is substituted by p-iodo-Phe-OH. Crystal structures reveal an overall folded conformation adopted by and. The former is folded in the type II beta-turn, which is stabilized by an intramolecular 1<--4 (formyl) C==O...H--N (Phe) hydrogen bond, whereas the latter is folded in an open turn without any intramolecular hydrogen bond. On the other hand, peptide has an extended conformation, and two different molecules in a crystallographic asymmetric unit form an antiparallel beta-sheet-like structure. In and, residues Ac8c and Dpg adopt left-handed helical and fully extended (C5) conformations, respectively. The cyclooctane ring in Ac8c acquires a boat-chair conformation. Crystal packing of is characterized by the association of aliphatic-aromatic rings via a C--H...pi interaction. In the crystal of, contrary to the usual observations, peptides are interlinked via networks of head-to-tail hydrogen bond and pi...pi interactions, which are generally observed to be mutually exclusive. The structure-function mechanism of the ligand-receptor interaction is discussed.
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528
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Crisma M, Moretto A, De Zotti M, Formaggio F, Kaptein B, Broxterman QB, Toniolo C. Turn stabilization in short peptides by C?-methylated ?-amino acids. Biopolymers 2005; 80:279-93. [PMID: 15612047 DOI: 10.1002/bip.20181] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The crystal-state conformations of three protected tripeptides, four tetrapeptides, and one pentapeptide, heavily based on the chiral C(alpha)-methylated alpha-amino acids Iva, (alpha Me)Nva, and (Me)Val, were assessed by X-ray diffraction analyses. The eight peptide sequences are as follows: Z-(D-Iva)2-D-Val-OMe, Z-D-Iva-L-Iva-Gly-OtBu, Z-L-Pro-D-Iva-L-Iva-Gly-OtBu, Z-L-Pro-L-Iva-D-Iva-Gly-OtBu, Z-Aib-[L-(alpha Me)Nva]2-OtBu, Ac-[L-(alpha Me)Val]3-D-(alpha Me)Val-OtBu, Z-[L-(alpha Me)Val]4-OH, and Z-L-Ala-[L-(alpha Me)Nva]4-OtBu. Two independent molecules were observed in the asymmetric units of Z-D-Iva-L-Iva-Gly-OtBu and Z-Aib-[L-(alpha Me)Nva]2-OtBu, while three independent molecules were seen in Z-L-Ala-[L-(alpha Me)Nva]4-OtBu. All peptides are folded in a single or multiple beta-turn conformations. Interestingly: (i) a water bridge within the N-terminal beta-turn is seen in Z-L-Pro-L-Iva-D-Iva-Gly-OtBu (dihydrate), and (ii) the hydroxyl group of the C-terminal carboxyl functionality of Z-[L-(alpha Me)Val]4-OH generates an oxy-analogue of a beta-turn. The N-terminal beta-turn is missing in molecules A and B, but it does occur, although poorly stabilized, in molecule C, of Z-L-Ala-[L-(alpha Me)Nva]4-OtBu.
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Affiliation(s)
- Marco Crisma
- Institute of Biomolecular Chemistry, CNR, Department of Chemistry, University of Padova, 35131 Padova, Italy.
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529
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Oba M, Tanaka M, Takano Y, Suemune H. Concise synthetic strategy toward cyclic α,α-disubstituted α-amino acids bearing a δ-nitrogen atom: chiral 1-substituted 4-aminopiperidine-4-carboxylic acids. Tetrahedron 2005. [DOI: 10.1016/j.tet.2004.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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530
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Polo F, Antonello S, Formaggio F, Toniolo C, Maran F. Evidence Against the Hopping Mechanism as an Important Electron Transfer Pathway for Conformationally Constrained Oligopeptides. J Am Chem Soc 2004; 127:492-3. [PMID: 15643851 DOI: 10.1021/ja043607e] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The rate constant of intramolecular electron transfer through oligopeptides based on the alpha-aminoisobutyric acid residue was determined as a function of the peptide length and found to depend weakly on the donor-acceptor separation. By measuring the electron-transfer activation energy and estimating the energy gap between donor and bridge, we were able to discard the electron hopping mechanism.
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Affiliation(s)
- Federico Polo
- Dipartimento di Scienze Chimiche, Università di Padova, via Marzolo 1, 35131 Padova, Italy
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531
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Improta R, Antonello S, Formaggio F, Maran F, Rega N, Barone V. Understanding Electron Transfer across Negatively-Charged Aib Oligopeptides. J Phys Chem B 2004; 109:1023-33. [PMID: 16866475 DOI: 10.1021/jp045797l] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The physicochemical effects modulating the conformational behavior and the rate of intramolecular dissociative electron transfer in phthalimide-Aibn-peroxide peptides (n = 0-3) have been studied by an integrated density functional/continuum solvent model. We found that three different orientations of the phthalimide ring are possible, labeled Phihel, PhiC7, and PhipII. In the condensed phase, they are very close in energy when the system is neutral and short. When the peptide chain length increases and the system is negatively charged, Phihel becomes instead the most stable conformer. Our calculations confirm that the 3(10)-helix is the most stable secondary structure for the peptide bridge. However, upon charge injection in the phthalimide end of the phthalimide-Aib3-peroxide, the peptide bridge can adopt an alpha-helix conformation as well. The study of the dependence of the frontier orbitals on the length and on the conformation of the peptide bridge (in agreement with experimental indications) suggests that for n = 3 the process could be influenced by a 3(10) --> alpha-helix conformational transition of the peptide chain.
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Affiliation(s)
- Roberto Improta
- Dipartimento di Chimica, Università di Napoli Federico II, Complesso Universitario Monte S. Angelo, Via Cintia, 80126 Napoli, Italy
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532
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Crisma M, Moretto A, Formaggio F, Kaptein B, Broxterman QB, Toniolo C. Meteoritic Cα-Methylated α-Amino Acids and the Homochirality of Life: Searching for a Link. Angew Chem Int Ed Engl 2004. [DOI: 10.1002/ange.200460908] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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533
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Crisma M, Moretto A, Formaggio F, Kaptein B, Broxterman QB, Toniolo C. Meteoritic C?-Methylated ?-Amino Acids and the Homochirality of Life: Searching for a Link. Angew Chem Int Ed Engl 2004; 43:6695-9. [PMID: 15593146 DOI: 10.1002/anie.200460908] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Marco Crisma
- Institute of Biomolecular Chemistry, CNR and Department of Chemistry, University of Padova via Marzolo 1, 35131 Padova, Italy
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534
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Synthesis and conformational properties of model dipeptides containing novel axially chiral α,β-didehydroamino acids at the (i+1) position of a β-turn conformation. Tetrahedron 2004. [DOI: 10.1016/j.tet.2004.09.066] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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535
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Jiménez AI, Ballano G, Cativiela C. First Observation of Two Consecutive γ Turns in a Crystalline Linear Dipeptide. Angew Chem Int Ed Engl 2004. [DOI: 10.1002/ange.200461230] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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536
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Jiménez AI, Ballano G, Cativiela C. First Observation of Two Consecutive γ Turns in a Crystalline Linear Dipeptide. Angew Chem Int Ed Engl 2004; 44:396-9. [PMID: 15538708 DOI: 10.1002/anie.200461230] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Ana I Jiménez
- Departamento de Química Orgánica, ICMA, Universidad de Zaragoza-CSIC, 50009 Zaragoza, Spain.
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537
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538
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Hanyu M, Murashima T, Miyazawa T, Yamada T. Synthesis of tripeptides containing a very crowded α,α-disubstituted glycine with pyridine rings by solid-phase Ugi reaction. Tetrahedron Lett 2004. [DOI: 10.1016/j.tetlet.2004.09.171] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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539
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Optimization of interactions in crystal packing revealed by crystal structures [ethyl 2-(formylamino)-3-thien-2-yl-2-(thien-2-ylmethyl)propanoate and ethyl 3-(5-bromothien-2-yl)-2-[(5-bromothien-2-yl)methyl]-2-(formylamino)propanoate]. J Mol Struct 2004. [DOI: 10.1016/j.molstruc.2004.06.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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540
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Peggion C, Formaggio F, Crisma M, Epand RF, Epand RM, Toniolo C. Trichogin: a paradigm for lipopeptaibols. J Pept Sci 2004; 9:679-89. [PMID: 14658789 DOI: 10.1002/psc.500] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Lipopeptaibols are members of a novel family of naturally occurring, short peptides with antimicrobial activity, characterized by a lipophilic acyl chain at the N-terminus, a high content of turn/helix inducing alpha-aminoisobutyric acid and a 1,2-amino alcohol at the C-terminus. Using solution methods, the prototypical lipopeptaibol trichogin GA IV and a large series of appropriately designed analogues were synthesized, which allow: (i) determination of the minimal lipid chain and peptide main-chain lengths for the onset of membrane activity, and (ii) exploitation of a number of physico-chemical techniques aimed at assessing the trichogin preferred conformation under a variety of conditions and at investigating its mechanism of interaction with the phospholipid membranes.
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Affiliation(s)
- Cristina Peggion
- Institute of Biomolecular Chemistry, CNR, Department of Organic Chemistry, University of Padova, 35131 Padova, Italy
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541
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Mazaleyrat JP, Wright K, Gaucher A, Toulemonde N, Wakselman M, Oancea S, Peggion C, Formaggio F, Setnicka V, Keiderling TA, Toniolo C. Induced Axial Chirality in the Biphenyl Core of the Cα-Tetrasubstituted α-Amino Acid Residue Bip and Subsequent Propagation of Chirality in (Bip)n/Val Oligopeptides. J Am Chem Soc 2004; 126:12874-9. [PMID: 15469284 DOI: 10.1021/ja040100v] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the dipeptides Boc-Bip-L-Val-OMe and Boc-Bip-D-Val-OMe, an induced axial chirality in the biphenyl core of the Bip residue, a conformationally labile, proatropoisomeric C(alpha,alpha)-disubstituted glycine, was observed by electronic CD and (1)H NMR. Chiral induction is significantly higher when the Val residue is located at the C-terminal position of Bip. An outstanding phenomenon of propagation of chirality was demonstrated to occur in the related 3(10)-helical -(Bip)n-L-Val (n = 2-6) oligopeptides by CD and vibrational CD techniques.
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Affiliation(s)
- Jean-Paul Mazaleyrat
- Contribution from SIRCOB, UMR CNRS 8086, Bâtiment Lavoisier, University of Versailles, F-78035 Versailles, France
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542
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Rowley DC, Kelly S, Jensen P, Fenical W. Synthesis and structure–activity relationships of the halovirs, antiviral natural products from a marine-derived fungus. Bioorg Med Chem 2004; 12:4929-36. [PMID: 15336272 DOI: 10.1016/j.bmc.2004.06.044] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2004] [Accepted: 06/28/2004] [Indexed: 11/20/2022]
Abstract
The halovirs are linear, lipophilic peptides produced by a marine-derived fungus of the genus Scytalidium. We recently reported that these molecules possess potent in vitro activity against the herpes simplex viruses 1 and 2. Here we present structure-activity relationships defining key structural elements for optimal viral inhibition. Results demonstrate that an N(alpha)-acyl chain of at least 14 carbons and an Aib-Pro dipeptide are critical for maintaining the antiviral activity.
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Affiliation(s)
- David C Rowley
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093-0204, USA.
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543
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Formaggio F, Peggion C, Crisma M, Kaptein B, Broxterman QB, Mazaleyrat JP, Wakselman M, Toniolo C. Recent contributions of electronic circular dichroism to the investigation of oligopeptide conformations. Chirality 2004; 16:388-97. [PMID: 15190584 DOI: 10.1002/chir.20051] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Recent applications in our laboratories of electronic circular dichroism to the study of peptide secondary structures and their changes under external stimuli are briefly reviewed. More specifically, this article deals with: 1). characterization of a novel peptide conformation; 2). origin of amino acid homo-chirality on Earth; 3). bend and helical peptides as spacers; and 4). transfer and propagation of chirality in peptides.
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Affiliation(s)
- Fernando Formaggio
- Institute of Biomolecular Chemistry, CNR, Department of Chemistry, University of Padova, Padova, Italy.
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544
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Formaggio F, Crisma M, Scipionato L, Antonello S, Maran F, Toniolo C. Synthesis and Characterization of a Series of Homooligopeptide Peroxyesters. Org Lett 2004; 6:2753-6. [PMID: 15281761 DOI: 10.1021/ol049028w] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A homologous series of stable N(alpha)-phthaloyl peptide peroxyesters based on alpha-aminoisobutyric acid residues was prepared. In each of the six oligomers synthesized, the chain of alpha-amino acids is separated from the peroxyester function by a beta-amino acid. [structure: see text]
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545
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Yang D, Zhang YH, Li B, Zhang DW, Chan JCY, Zhu NY, Luo SW, Wu YD. Effect of Side Chains on Turns and Helices in Peptides of β3-Aminoxy Acids. J Am Chem Soc 2004; 126:6956-66. [PMID: 15174865 DOI: 10.1021/ja049976s] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have investigated, using NMR, IR, and CD spectroscopy and X-ray crystallography, the conformational properties of peptides 1-10 of beta(3)-aminoxy acids (NH(2)OCHRCH(2)COOH) having different side chains on the beta carbon atom (e.g., R = Me, Et, COOBn, CH(2)CH(2)CH=CH(2), i-Bu, i-Pr). The beta N-O turns and beta N-O helices that involve a nine-membered-ring intramolecular hydrogen bond between NH(i)(+2) and CO(i), which have been found previously in peptides of beta(2,2)-aminoxy acids (NH(2)OCH(2)CMe(2)COOH), are also present in those beta(3)-aminoxy peptides. X-ray crystal structures and NMR spectral analysis reveal that, in the beta N-O turns and beta N-O helices induced by beta(3)-aminoxy acids, the N-O bond could be either anti or gauche to the C(alpha)-C(beta) bond depending on the size of the side chain; in contrast, only the anti conformation was found in beta(2,2)-aminoxy peptides. Both diamide 1 and triamide 9 exist in different conformations in solution and in the solid state: parallel sheet structures in the solid state and predominantly beta N-O turn and beta N-O helix conformations in nonpolar solvents. Theoretical studies on a series of model diamides rationalize very well the experimentally observed conformational features of these beta(3)-aminoxy peptides.
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Affiliation(s)
- Dan Yang
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
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546
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Formaggio F, Barazza A, Bertocco A, Toniolo C, Broxterman QB, Kaptein B, Brasola E, Pengo P, Pasquato L, Scrimin P. Role of Secondary Structure in the Asymmetric Acylation Reaction Catalyzed by Peptides Based on Chiral Cα-Tetrasubstituted α-Amino Acids. J Org Chem 2004; 69:3849-56. [PMID: 15153018 DOI: 10.1021/jo040107v] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In a recent series of papers, Miller and co-workers were able to show that His(pi-Me)-based, terminally protected peptides are potent catalysts of the asymmetric acyl transfer reaction, useful for the kinetic resolution of alcohols. In a structure-supporting solvent, one of the most active compounds, an Aib-containing tetrapeptide, is folded in a doubly intramolecularly H-bonded beta-hairpin motif incorporating a type-II' beta-turn conformation. In this work, we have expanded the study of the Miller tetrapeptide by examining a set of analogues and shorter sequences (dipeptide amides), characterized by chiral C(alpha)-tetrasubstituted alpha-amino acids of diverging bulkiness and optical configuration. Peptide synthesis in solution, conformational analysis by FT-IR absorption and (1)H NMR techniques, and screening of catalytic activity as well have been performed. Our results confirm the close relationship between the beta-hairpin 3D-structure and the catalytic activity of the peptides. A tetrapeptide analogue slightly more selective than the Miller compound has been found. However, the terminally protected, industrially more appealing, dipeptide amides are poorly effective.
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Affiliation(s)
- Fernando Formaggio
- Department of Chemistry, University of Padova, and ICB, CNR, 35131 Padua, Italy
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547
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Rathore RS, Narasimhamurthy T. Structural Features in the Model of a Thermostable and Stress-resistant Protein, SP1 from aspen. J Biomol Struct Dyn 2004; 21:651-5. [PMID: 14769057 DOI: 10.1080/07391102.2004.10506955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
A three dimensional theoretical model of SP1 (stable protein 1), which is resistant to high temperature and biotic-stresses, is presented here. The model was generated by the application of homology modeling technique. The conformational rigidity imparted to the fold by the presence of hydrogen-bonded, C5, C7, C10 and C13 structures in the loop regions, multiple aromatic--aromatic interactions at the protein interior and on the surface, in addition to salt-links and hydrogen-bonds are primarily the major factors, responsible for the increased stability of protein. The putative protein family is characterized by motifs, E-x(0,1)-L-x-[AEGQS] and V-x(2,3)-L-x-[ADEGST] and the active site in the tertiary structure is formed by conserved aromatic and isoleucine clusters.
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548
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Saviano M, Improta R, Benedetti E, Carrozzini B, Cascarano GL, Didierjean C, Toniolo C, Crisma M. Benzophenone Photophore Flexibility and Proximity: Molecular and Crystal-State Structure of a Bpa-Containing Trichogin Dodecapeptide Analogue. Chembiochem 2004; 5:541-4. [PMID: 15185380 DOI: 10.1002/cbic.200300811] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Michele Saviano
- Institute of Biostructures and Bioimaging, CNR via Mezzocannone 6, 80134 Napoli, Italy.
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549
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Formaggio F, Moretto V, Crisma M, Toniolo C, Kaptein B, Broxterman QB. New tools for the control of peptide conformation: the helicogenic Cα-methyl, Cα-cyclohexylglycine*. ACTA ACUST UNITED AC 2004; 63:161-70. [PMID: 15009538 DOI: 10.1111/j.1399-3011.2003.00123.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The novel Calpha-tetrasubstituted alpha-amino acid Calpha-methyl, Calpha-cyclohexylglycine was prepared by hydrogenation of its Calpha-methyl, Calpha-phenylglycine precursor. Terminally protected homodi-, homotri-, and homotetrapeptides from Calpha-methyl, Calpha-cyclohexylglycine and co-oligopeptides to the pentamer level in combination with Gly or alpha-aminoisobutyric acid residues were prepared by solution methods and fully characterized. The results of a conformational analysis, performed by use of Fourier transform infrared (FT-IR) spectrophotometer absorption, 1H NMR, and X-ray diffraction techniques, support the contention that this Calpha-methylated, Cbeta-trisubstituted aliphatic alpha-amino acid is an effective beta-turn and 3(10)-helix inducer in tri- and longer peptides as its Calpha-methyl valine parent compound, but partially divergent from the corresponding aromatic Calpha-methyl, Calpha-diphenylmethylglycine residue, known to promote folded and fully extended structures to a significant extent in these oligomers.
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Affiliation(s)
- F Formaggio
- Institute of Biomolecular Chemistry, CNR, Department of Organic Chemistry, University of Padova, 35131 Padova, Italy.
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550
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Formaggio F, Oancea S, Peggion C, Crisma M, Toniolo C, Wright K, Wakselman M, Mazaleyrat JP. New tools for the control of peptide conformation and supramolecular chemistry: Crown-carrier, Cα-methyl L-DOPA amino acids. Biopolymers 2004; 71:667-74. [PMID: 14991676 DOI: 10.1002/bip.10594] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The preferred conformation of five, terminally protected, model peptide series to the hexamer level, based on three novel crowned, C(alpha)-methyl L-DOPA amino acids combined with either L-Ala/Aib or Gly/Aib, were assessed in structure supporting solvents using FT-IR absorption, (1)H NMR, and CD techniques. The FT-IR absorption spectra strongly suggest that the contribution of the crowned C(alpha)-tetrasubstituted residue to intramolecular H-bonding is equivalent to that of Aib and is much more significant than that of either L-Ala or Gly. In addition, the (1)H NMR titrations and the CD patterns resemble those typically exhibited by (right-handed) 3(10)-helical structures.
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Affiliation(s)
- Fernando Formaggio
- Institute of Biomolecular Chemistry, CNR, Department of Organic Chemistry, University of Padova, 35131 Padova, Italy.
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