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  • 310-helix  (4)
  • β-turn  (3)
  • molecular dynamics  (2)
  • 1
    ISSN: 1075-2617
    Keywords: β-bend ; 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 dodecamer level) from the small-ring alicyclic Cα,α-dialkylated glycine 1-aminocyclobutane-1-carboxylic acid (Ac4c) and two Ala/Ac4c tripeptides were 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 Z-Ac4c-OH and Z2-Ac4c-OH, the tripeptides Z-(Ac4c)3-OtBu, Z-Ac4c-(L-Ala)2-OMe and Z-L-Ala-Ac4c-L-Ala-OMe, and the tetrapeptide Z-(Ac4c)4-OtBu were determined in the crystal state by X-ray diffraction. The average geometry of the cyclobutyl moiety of the Ac4c residue was assessed and the τ(N-Cα-C′) bond angle was found to be significantly expanded from the regular tetrahedral value. The conformational data are strongly in favour of the conclusion that the Ac4c residue is an effective β-turn and helix former. A comparison with the structural propensities 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, 5-8) is made and the implications for the use of the Ac4c residue in conformationally constrained peptide analogues are briefly examined. © 1997 European Peptide Society and John Wiley & Sons, Ltd
    Additional Material: 8 Ill.
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  • 2
    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
    Additional Material: 10 Ill.
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  • 3
    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.
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  • 4
    ISSN: 1075-2617
    Keywords: (αMe) amino acids ; CD spectroscopy ; 310-helix ; peptide 3D-structure ; X-ray structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The terminally blocked tetrapeptide pBrBz-[D-(αMe)Leu]2-D-(αMe)Val-D-(αMe)Leu-OtBu is folded in the crystal state in a left-handed 310-helical structure stabilized by two consecutive 1 ← 4 C=O⃛H—N intramolecular H-bonds, as determined by X-ray diffraction analysis. A CD study strongly supports the view that this conformation is also that largely prevailing in MeOH solution. A comparison with the published conformation of pBrBz-[D-(αMe)Leu]4-OtBu indicates that incorporation of a single internal β-branched (αMe)Val guest residue into the host homo-tetrapeptide from the γ-branched (αMe)Leu residue is responsible for a dramatic structural perturbation, i.e. an inversion of the 310 screw sense from right to left-handed.
    Additional Material: 2 Ill.
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  • 5
    ISSN: 1075-2617
    Keywords: Cα,α-disubstituted amino acids ; crystal structure ; molecular dynamics ; conformation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The crystal structures of three fully protected tripeptides containing the Dφg residue (Cα,α-diphenylglycine) in the central position are reported, namely Z-Gly-Dφg-Gly-OMe (a), Z-Gly-Dφg-Aib-OMe (b) and Z-Aib-Dφg-Aib-OMe (c). The molecular conformations are quite unusual because the Dφg residue adopts a folded conformation in the 310-helical region when the following residue adopts a folded conformation of opposite handedness (peptidesbandc). In contrast, the Dφg residue adopts the more frequently observed fully extended conformation when the following residue adopts a semi-extended conformation (peptidea). These findings are in agreement with the theoretical calculations on Ac-Dφg-Aib-NHCH3 and Ac-Aib-Dφg-NHCH3 also reported in this work. © 1998 European Peptide Society and John Wiley & Sons, Ltd.
    Additional Material: 9 Ill.
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  • 6
    ISSN: 1075-2617
    Keywords: β-bend ; cyclic amino acid ; 310-helix ; peptide conformation ; X-ray diffraction ; Chemistry ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A complete series of terminally blocked, monodispersed homo-oligopeptides (to the pentamer level) from the sterically demanding, medium-ring alicyclic Cα,α-disubstituted glycine 1-aminocyclooctane-1-carb oxylic acid (Ac8c), and two Ala/Ac8c tripeptides, were synthesized by solution methods and fully characterized. The preferred conformation of all the oligopeptides was determined in deuterochloroform solution by IR absorption and 1H-NMR. The molecular structures of the amino acid derivative Z-Ac8c-OH, the dipeptide pBrBz- (Ac8c)2-OH and the tripeptide pBrBz-(Ac8c)3-OtBu were assessed in the crystal state by X-ray diffraction. Conformational energy computations were performed on the monopeptide Ac-Ac8c-NHMe. Taken together, the results obtained strongly support the view that the Ac8c residue is an effective β-turn and helix former. A comparison is also made with the conformational preferences of α-aminoisobutyric acid, the prototype of Cα, α-disubstituted glycines, and of the other members of the family of 1-aminocycloalkane-1-carboxylic acids (Acnc, with n=3, 5-7) investigated so far. The implications for the use of the Ac8c residue in peptide conformational design are considered.
    Additional Material: 8 Ill.
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  • 7
    ISSN: 0006-3525
    Keywords: molecular scaffolds ; β-turn ; tachykinin antagonist ; x-ray ; nmr ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We recently reported the rational design, synthesis, and structural characterization of the most potent and selective peptide-based neurokinin A antagonist thus far described: cyclo(Met1-Asp2-Trp3-Phe4-Dap5-Leu6)cyclo(2β-5β). Its bicyclic structure is characterized by a type I and a type II two β-turn around Trp3-Phe4 and Leu6-Met1, respectively. In order to understand whether the two different β-turned structures are determined by the bicyclic structure or by the amino acid type at the corner positions, we have synthesized the pseudosymmetrical analogue cyclo(Phe1-Asp2-Trp3-Phe4-Dap5-Trp6)cyclo(2β-5β). The structural characterization in the crystal state and in solution, here reported, gives an experimental evidence that the backbone of the bicyclic structure is a rigid scaffold that can be used to build both a type I and type II β-turn independently from the amino acid composition. © 1997 John Wiley & Sons, Inc. Biopoly 40: 505-518, 1996
    Additional Material: 8 Ill.
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  • 8
    ISSN: 0006-3525
    Keywords: cyclic peptides ; molecular dynamics ; nmr ; conformation ; FK506 ; FK506 binding proteins ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The conformational behavior in solution of a cyclic peptide with sequence cyclo-(Pro1-Pro2-Dab3 (cHexA)ψ[N7HCO]-Leu4ψ[NHCO]-Suc5-Gly6-) has been throughly investigated with the combined use of nmr and molecular dynamic techniques. The compound, which has been modeled to mimic the FK506 macrolide bound to the FK506 binding protein structure, can be considered as a peptidic analogue of the FK506 system.The synthesis was carried out on a phenylacetoamidomethyl resin using an appropriate protocol for the peptide chain elongation. The conformational properties of the cyclic hexapeptide were studied in DMSO and water. The nmr data in DMSO and restrained molecular dynamics simulations show the presence of two contiguous cis peptide bonds involving the -Gly-Pro-Pro- segment. This segment in water exhibits conformational heterogeneity presenting at least two distinct conformational families, characterized the first by cis-cis and the second by a trans-cis Gly-Pro-Pro configuration; the trans-cis isomer was fully characterized. © 1997 John Wiley & Sons, Inc. Biopoly 42: 349-361, 1997
    Additional Material: 6 Ill.
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