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  • Polymer and Materials Science  (22)
  • β-turn  (3)
  • 1
    Electronic Resource
    Electronic Resource
    Conformational characterization of peptides rich in the cycloaliphatic Cα,α-disubstituted glycine 1-amino-cyclononane-1-carboxylic acid (1997)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Peptide Science 3 (1997), S. 367-382 
    Details
    ISSN: 1075-2617
    Keywords: β-turn ; cyclic amino acid ; 310-helix ; peptide conformation ; X-ray diffraction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A series of N- and C-protected, monodispersed homo-oligopeptides (to the pentamer level) from the cycloaliphatic Cα,α,-dialkylated glycine 1-aminocyclononane-1-carboxylic acid (Ac9c) and two Ala/Ac9c tripeptides have been synthesized by solution methods and fully characterized. The conformational preferences of all the model peptides were determined in deuterochloroform solution by FT-IR absorption and 1H-NMR. The molecular structures of the amino acid derivatives mClAc-Ac9c-OH and Z-Ac9c-OtBu, the dipeptide pBrBz-(Ac9c)2-OtBu, the tetrapeptide Z-(Ac9c)4-OtBu, and the pentapeptide Z-( Ac9c)5-OtBu were determined in the crystal state by X-ray diffraction. Based on this information, the average geometry and the preferred conformation for the cyclononyl moiety of the Ac9c residue have been assessed. The backbone conformational data are strongly in favour of the conclusion that the Ac9c residue is a strong β-turn and helix former. A comparison with the structural propensity of α-aminoisobutyric acid, the prototype of Cα,α-dialkylated glycines, and the other extensively investigated members of the family of 1-aminocycloalkane-1-carboxylic acids (Acnc, with n=3-8) is made and the implications for the use of the Ac9c residue in conformationally constrained analogues of bioactive peptides are briefly examined. © 1997 European Peptide Society and John Wiley & Sons, Ltd.J. Pep. Sci. 3: 367-382No. of Figures: 10. No. of Tables: 6. No. of References: 62
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  • 2
    Electronic Resource
    Electronic Resource
    Conformational studies on synthetic peptides reproducing the dibasic processing site of pro-ocytocin-neurophysin (1995)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Peptide Science 1 (1995), S. 251-265 
    Details
    ISSN: 1075-2617
    Keywords: Hormone biosynthesis ; ocytocin ; prohormone ; proteolytic processing ; β-turn ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Synthetic peptides reproducing the proteolytic processing site of pro-ocytocin were studied by different spectroscopic techniques, including circular dichroism, Fourier tranform infrared absorption, and mono and bidimensional nuclear magnetic resonance, in order to ascertain the possible role of three-dimensional structure in the recognition process by maturation enzymes. Experimental results were compared with energy minimization calculations and suggest that: (i) the region situated on the N-terminus of the Lys-Arg doublet may form a β-turn; (ii) the sequential organization of the residues participating in the β-turn determines the privileged relative orientation of the basic amino acid sidechains and the subtype of turn; and (iii) the peptide segment situated on the C-terminal side of the dibasic doublet may assume a helix arrangement. These findings, in spite of the limitations connected to the flexibility of linear peptides, seem to substantiate the hypothesis that structural motifs around the cleavage site could be important for recognition and processing. However, a straightforward correlation between details of the secondary structure and the in vitro reactivity toward a putative convertase is not yet possible.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/psc.310010406
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  • 3
    Electronic Resource
    Electronic Resource
    Bicyclic peptides: Solid state conformation of cyclo(Glu-Leu-Pro-Gly-Lys-Leu-Pro-Gly)cyclo(1γ-5∊)Gly (1990)
    New York : Wiley-Blackwell
    Biopolymers 30 (1990), S. 509-516 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The solid state conformational analysis of the ionophoric homodetic bicyclic cyclo(Glu-Leu-Pro-Gly-Lys-Leu-Pro-Gly)cyclo(1γ-5∊)Gly (BCP3) has been carried out by x-ray diffraction. It crystallizes with 4.5 molecules of water per peptide molecule in the monoclinic system, space group P21, with a = 11.425 Å, b = 16.616 Å, c = 13.931 Å, β = 109.24°, and Z = 2. The structure has been determined by direct methods and refined to an R factor of 0.061 for 2448 observed reflections. The structure characterized by all trans peptide bonds is stabilized by three intramolecular hydrogen bonds: a type II β-turn, a mixed type I-type III β-turn, and a pseudo γ-turn, which involves the side chain C=O and the main-chain N—H groups of the Glu1 residue. The resulting globular molecule presents a rather hydrophilic surface with most of the C=O groups available to hydration of the solvent molecules, which are linked through hydrogen bonds of the N—H … O or O—H … O types in a complicated H-bonding scheme. The conformation observed in the solid state is rather different from the conformation proposed in solution for both the free and the Ca2+-complexed BCP3 molecule.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360300504
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  • 4
    Electronic Resource
    Electronic Resource
    Stereochemical behavior of acyclic peptide-cation complexes (1990)
    New York : Wiley-Blackwell
    Biopolymers 30 (1990), S. 197-204 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The role of the β-turns in the peptide interaction with several cations was investigated. In this work we report the solution studies of four linear peptides: Z-Aib-Aib-Aib-L-Val-OMe, Boc-D-alle-L-Ile-D-alle-L-Ile-OMe, Boc-L-Leu-L-Leu-L-Leu-L-Leu-OMe, and Boc-L-Phe-B-Phe-L-Phe-D-Phe-OMe.CD and 1H-nmr spectra reveal the presence of multiple ion-bounding equilibria. The stoichiometry and binding constant of the four peptide in the presence of Ca2+ ions in acetonitrile solution has been determined.Variable-temperature nmr spectra in the absence and in thepresence of a large excess of cation have shown that the complexation process is not critically dependent on the conformation of the peptide.
    Additional Material: 9 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360300119
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  • 5
    Electronic Resource
    Electronic Resource
    Ion binding of cyclolinopeptide A: An nmr and CD conformational study (1991)
    New York : Wiley-Blackwell
    Biopolymers 31 (1991), S. 761-767 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: CD and nmr techniques have been used to study, in acetonitrile solution, the ion-complexing capability of Cyclolinopeptide A (CLA), a cyclic nonapeptide of sequence \documentclass{article}\pagestyle{empty}\begin{document}$$ cyclo{\rm - }\left({{\rm Pro - Pro - Phe - Phe - Leu - Ile - Ile - Leu - Val}} \right) $$\end{document} endowed with remarkable cytoprotective ability in vitro, and the conformation of the Ba2+/ CLA complex.At room temperature, CLA in acetonitrile shows a proton nmr spectrum characteristic of the coexistence of many different conformers in intermediate exchange. The backbone contains a cis Pro-Pro bond, with all other peptide bonds in the transconformation.CLA binds Ba2+ more tightly than the other cations studied, namely K+, Na+, Mg2+, and Ca2+; CD data are indicative of the presence of both 1 : 2 (sandwich) and 1 : 1 (equimolar) type complexes, depending on the Ba2+ ion concentration, whereas nmr data are consistent with an equimolar form.The relevant conformational features of the equimolar Ba2+/CLA complex are that the backbone contains all transpeptide bonds, a type I 6 → 3 β-turn and a 3 → 1 γ-turn (or a distorted 3 → 9 β-turn). The global shape of the complexed peptide can be described as a bowl, with the concave (polar) side hosting Ba2+ and the convex side predominantly apolar.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360310621
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  • 6
    Electronic Resource
    Electronic Resource
    Defect peptide chemistry: Perturbations in the structure of a homopentapeptide induced by a guest residue interrupting side-chain regularityDedicated to Prof. Murray Goodman on the occasion of his 65th birthday. (1994)
    New York : Wiley-Blackwell
    Biopolymers 34 (1994), S. 1409-1418 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The fully blocked pentapeptide Tfa-(Deg)2-L-Abu-(Deg)2-OtBu (Tfa:triflouroacetyl; Deg: Cα,α-diethylglycine; OtBu: tert-butoxy) adopts in the crystal state a regular, right-handed 310-helical structure stabilized by three N — H … O = C intramolecular 1 ← 4 (or C10) H bonds, as determined by an x-ray diffraction analysis. However, a Fourier transform ir absorption and 1H-nmr study strongly supports the view that in deuterochloroform solution the four Deg residues at both termini of the peptide main chain are involved in successive, fully extended C5 forms. A comparison with the stable, fully developed, multiple C5 conformation of Tfa-(Deg)5-OtBu indicates that incorporation of an Abu guest residue, interrupting the side-chain uniformity of the host (Deg)5 homopeptide, while altering only marginally the conformation in a solvent of low polarity, is responsible for a dramatic perturbation of the crystal-state structure. © 1994 John Wiley & Sons, Inc.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360341012
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  • 7
    Electronic Resource
    Electronic Resource
    A crystal structure with features of an antiparallel α-pleated sheet (1994)
    New York : Wiley-Blackwell
    Biopolymers 34 (1994), S. 1463-1468 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A single-crystal x-ray diffraction analysis of Boc-L-Ala-D-aIle-L-Ile-OMe has been carried out. The analysis has shown (a) that the tripeptide molecules have in part an α-extended conformation, the torsion angles of the L-Ala and D-aIle residues being ϕ1 = -75.1° and ψ1 = -25.8° and ϕ2 = 67.3° and ψ2 = 44.1°, respectively, and (b) that the molecules are organized in rippled planes where they occur in relative antiparallel orientation linked together side by side by H bonds. This molecular organization of the tripeptide corresponds closely to that of an antiparallel α-pleated sheet, and likely constitutes the first example of a structure of this kind for which a characterization at the atomic level has been achieved. A molecular dynamics study has shown that the molecular conformation of the tripeptide in the crystalline state is determined primarily by intermolecular interactions. © 1994 John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360341103
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  • 8
    Electronic Resource
    Electronic Resource
    Conformational studies of heterochiral peptides with diastereoisomeric residues: Crystal and molecular structures of linear dipeptides derived from leucine, isoleucine, and allo-isoleucine (1995)
    New York : Wiley-Blackwell
    Biopolymers 36 (1995), S. 401-408 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The x-ray diffraction analyses of three N- and C-terminally blocked L, D dipeptides, namely t-Boc-D-Leu-L-Leu-OMe (1), t-Boc-L-Ile-D-alle-OMe (2), and t-Boc-D-aIle-L-Ile-OMe (3) containing enantiomeric or diastereomeric amino acid residues have been carried out. The structures were determined by direct methods and refined anisotropically to final R factors of 0.077. 0.058. and 0.072 for (1) (2) and (3), respectively.Peptides 1-3 all assume a similar U-shaped structure with φ and ψ torsion angles cosrresponding to one of the possible calculated minimum energy regions (regions E and G for L residues, and F*. D* and H* for D residues). The peptide backbones of 1-3 are almost super-imposable [provided that the appropriate inversion of the chiral centers of (2) is made].Side-chain conformations of Leu residues in peptide (1) are g- (tg-) for the L-Leu residue and the mirrored g+ (tg+) for the D-Leu residue; however, in peptides (2) and (3) the conformations of the isoconfiguralional side chains of the Ile or allo-Ile residues are (g-t) t and (tg+) tfor the L-Ile and the D-allo-Ile moieties, respectively. In all cases, these conformations correspond to the more populated conformers of β-branched residues statistically found in crystal structures of small peptides.The results seem to indicate that, at least in short peptides with enantiomeric or diastereoisomeric residues, the change in chirality in the main-chain atoms perturbs the backbone conformation to a lesser extent and the side chain conformation to a greater extent. © 1995 John Wiley & Sons, Inc.
    Additional Material: 7 Ill.
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    URL: http://dx.doi.org/10.1002/bip.360360403
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  • 9
    Electronic Resource
    Electronic Resource
    Discovering protein secondary structures: Classification and description of isolated α-turns (1996)
    New York : Wiley-Blackwell
    Biopolymers 38 (1996), S. 705-721 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Irregular protein secondary structures are believed to be important structural domains involved in molecular recognition processes between proteins, in interactions between peptide substrates and receptors, and in protein folding. In these respects tight turns are being studied in detail. They also represent template structures for the design of new molecules such as drugs, pesticides, or antigens. Isolated α-turns, not participating in α-helical structures, have received little attention due to the overwhelming presence of other types of tight turns in peptide and protein structures. The growing number of protein X-ray structures allowed us to undertake a systematic search into the Protein Data Bank of this uncharacterized protein secondary structure. A classification of isolated α-turns into different types, based on conformational similarity, is reported here. A preliminary analysis on the occurrence of some particular amino acids in certain positions of the turned structure is also presented. © 1996 John Wiley & Sons, Inc.
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  • 10
    Electronic Resource
    Electronic Resource
    Solvent-mediated conformational transition in β-alanine containing cyclic peptides. VIIIprevious parts of this series are in Refs 1-7. (1996)
    New York : Wiley-Blackwell
    Biopolymers 38 (1996), S. 693-703 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In the present paper we describe the solution nmr structural analysis and restrained molecular dynamic simulation of the cyclic pentapeptide cyclo-(Pro-Phe-Phe-β-Ala-β-Ala). The conformational analysis carried out in CD3CN and dimethylsulfoxide (DMSO) solutions by nmr spectroscopy was based on interproton distances derived from rotating frame nuclear Overhauser effect spectroscopy spectra and homonuclear coupling constants. A restrained molecular dynamic simulation in vacuo was also performed to build refined molecular models. The molecule is present in both solvent systems as two slowly interconverting conformers, characterized by a cis-trans isomerism around the β-Ala5-Pro1 peptide bond. In CD3CN solution, the conformer with a cis peptide bond is quite similar to that observed in the solid state, while the conformer containing all trans peptide bonds is characterized by an intramolecular hydrogen bond stabilizing a C10- and a C13-ring structure. In DMSO solution, the trans isomer is partly similar to that observed in CD3CN solution while the cis isomer is different from that observed in the solid state. The effect of the solvent in stabilizing different conformations was also investigated in DMSO-CD3CN solvent mixtures. © 1996 John Wiley & Sons, Inc.
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