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  • 1
    Electronic Resource
    Electronic Resource
    Conformational investigation of a novel, dipeptide based molecular scaffold (1998)
    Springer
    International journal of peptide research and therapeutics 5 (1998), S. 151-153 
    Details
    ISSN: 1573-3904
    Keywords: benzodiazepine ; coupling constants ; distance geometry ; ensemble dynamics ; Karplus equation ; molecular scaffold
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The conformational features of a novel, dipeptide-based molecular scaffold are described. Four model systems of a trisubstituted 1,4-diazepine-3-one system, varying in the chirality and amino acid within the ring system, have been investigated by high-resolution NMR and metric-matrix distance geometry calculations. Because of the small number of protons within the scaffold, nuclear Overhauser effects provide only limited conformational information. Instead, extensive use of scalar1 H-1H and 1H-13C coupling constants was utilized in the refinement. The resulting conformations of the model systems provide insight into the expected topological orientations of the amino acids or chemical functionalities attached to the seven-membered ring system, the first step of the utilization of this scaffold in the rational design of peptidomimetics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1008852029052
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  • 2
    Electronic Resource
    Electronic Resource
    Conformational investigation of a novel dipeptide based molecular scaffold (1998)
    Springer
    International journal of peptide research and therapeutics 5 (1998), S. 151-153 
    Details
    ISSN: 1573-3904
    Keywords: benzodiazepine ; coupling constants ; distance geometry ; ensemble dynamics ; Karplus equation ; molecular scaffold
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary The conformational features of a novel, dipeptide-based molecular scaffold are described. Four model systems of a trisubstituted 1,4-diazepine-3-one system, varying in the chirality and amino acid within the ring system, have been investigated by high-resolution NMR and metric-matrix distance geometry calculations. Because of the small number of protons within the scaffold, nuclear Overhauser effects provide only limited conformational information. Instead, extensive use of scalar1H−H1 and1H−13C coupling constants was utilized in the refinement. The resulting conformations of the model systems provide insigh into the expected topological orientation of the amino acids or chemical functionalities and attached to the seven-membered ring system, the first step of the utilization of this scaffold in the rational design of peptidomimetics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02443459
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  • 3
    Electronic Resource
    Electronic Resource
    1,2,5-Trisubstituted 1,4-diazepine-3-one: A novel dipeptidomimetic molecular scaffold (1998)
    Springer
    International journal of peptide research and therapeutics 5 (1998), S. 83-86 
    Details
    ISSN: 1573-3904
    Keywords: 1,4-diazepine-3-one ; dipeptidomimetic ; molecularscaffold
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The continuing effort to transform bioactive peptides into non-peptide peptidomimetics of therapeutic potential requires a diversity of tools such as molecular scaffolds, pseudopeptide modifications, and conformation mimetics. To this end, a novel polyfunctional monoheterocyclic system, 1,2,5-trisubstituted hexahydro-3-oxo-1H-1,4-diazepine ring (DAP), was designed. The linear precursor for the DAP was generated through a reductive alkylation step including a modified side chain and an α-amino function of two amino acid derivatives. Structural analysis of model diastereomeric DAPs, employing 1H and13 C NMR and computer simulation, revealed the conformational preferences of this system. The structural similarities to the 1,4-benzodiazepine, a common molecular scaffold for many non-peptidic peptidomimetic agents, and the pronounced dipeptidomimetic character of the DAP system offer a new powerful tool to medicinal chemists engaged in rational peptide-based drug design.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1008864610626
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  • 4
    Electronic Resource
    Electronic Resource
    1,2,5-Trisubstituted 1,4-diazepine-3-one: A novel dipeptidomimetic molecular scaffold (1998)
    Springer
    International journal of peptide research and therapeutics 5 (1998), S. 83-86 
    Details
    ISSN: 1573-3904
    Keywords: 1,4-diazepine-3-one ; dipeptidomimetic ; molecular scaffold
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary The continuing effort to transform bioactive peptides into non-peptide peptidomimetics of therapeutic potential requires a diversity of tools such as molecular scaffolds, pseudopeptide modifications, and conformation mimetics. To this end, a novel polyfunctional monoheterocyclic system, 1,2,5-trisubstituted hexahydro-3-oxo-1H-1,4-diazepine ring (DAP), was designed. The linear precursor for the DAP was generated through a reductive alkylation step including a modified side chain and an α-amino function of two amino acid derivatives. Structural analysis of model diastereomeric DAPs, employing1H and13C NMR and computer simulation, revealed the conformational preferences of this system. The structural similarities to the 1,4-benzodiazepine, a common molecular scaffold for many non-peptidic peptidomimetic agents, and the pronounced dipeptidomimetic character of the DAP system offer a new powerful tool to medicinal chemists engaged in rational peptide-based drug design.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02443444
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  • 5
    Electronic Resource
    Electronic Resource
    Conformational Analysis by NMR and Distance-Geometry Techniques of Deltorphin Analogs (1998)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 1998 (1998), S. 2279-2287 
    Details
    ISSN: 1434-193X
    Keywords: Receptor selectivity ; Agonist activity ; Distance geometry ; Conformation ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: To identify the peptide conformation that is preferentially recognized by the receptor, we have synthetized by solid-phase method a series of deltorphin I analogs with increasing selectivity for δ- and μ-opioid receptor. Structure-selectivity relationship of these peptides were evaluated on the basis of receptor-binding properties and conformational features, computed by two-dimensional NMR spectra and distance-geometry techniques. These compounds in solution are present with a large number of conformers with no defined secondary structural elements. The analysis of the average properties of these compounds indicate the presence of some distinct conformational preferences that can be related to the observed opioid receptor selectivities. Selectivity for the δ- and μ-opioid receptors can be ascribed to the spatial arrangement of the aromatic moieties. In addition, substitutions in position 2 and 4 are important for the correct arrangement and must be taken into account in the design of δ-opioid receptor-selective ligands.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    Conformational characterization of a peptide mimetic of the third cytoplasmic loop of the G-protein coupled parathyroid hormone/parathyroid hormone related protein receptor (1996)
    New York : Wiley-Blackwell
    Biopolymers 40 (1996), S. 653-666 
    Details
    ISSN: 0006-3525
    Keywords: parathyroid hormone ; parathyroid hormone-related protein ; G-protein coupled receptors ; peptide conformations in micelles ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The third-cytoplasmic loop of the G-protein coupled receptor responsible for the activity of parathyroid hormone and parathyroid hormone-related protein has been structurally characterized in aqueous solution in the presence of sodium dodecylsulfate and dodecylphosphocholine micelles. The high-resolution conformation of the 29-amino acid peptide containing the sequence of the cytoplasmic loop was obtained by CD and nmr. The structure was refined using a two-step distance geometry based method that first includes the removal of all side chains to quickly locate the globular fold of the peptide. After a simulated annealing protocol, the side chains are added in a random fashion. The resulting conformation was further refined with nuclear Overhauser enhancement restrained molecular dynamics using a two-phase simulation cell consisting of carbon tetrachloride and water as a mimetic of the biphasic, hydrophobic/hydrophilic character of the micelles in which the experimental measurements were carried out. The topological orientation of the cycloplasmic loop within the micelle was determined by addition of 5-doxylstearate and monitoring the decrease of nmr signal intensities from the radical-induced relaxation. The conformation and relative orientation of the peptide provided insight into the mechanism by which the cytoplasmic portion of the receptor activates the heterotrimeric, guanine nucleotide-binding regulatory protein, one of the first steps in signal transduction. © 1997 John Wiley & Sons, Inc. Biopoly 40: 653-666, 1996
    Additional Material: 12 Ill.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    Structure, dynamics, and topological orientation of the polyether, ionophore antibiotic monensin, in a micellar environment (1997)
    New York : Wiley-Blackwell
    Biopolymers 42 (1997), S. 759-769 
    Details
    ISSN: 0006-3525
    Keywords: antibiotic, conformation of antibiotic ; nmr structure refinement ; cation transport ; micelles ; structure in micelles ; spectroscopy in micelles ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The structure and dynamics of the ionophoric antibiotic monensin in the presence of micelles have been determined. The conformation of monensin was derived from 50 nuclear Overhauser enhancement (NOE) derived distance restraints and metric-matrix based distance geometry calculations. The conformation was further refined with extensive NOE restrained molecular dynamics simulations carried out in a biphasic simulation cell. From the addition of doxylstearate and monitoring of the induced relaxation of the nmr signals, the relative topological orientation of the molecule within the micelle was ascertained. The results indicate two dihedral angles that act as hinge regions allowing the molecule to adopt a wide range of conformations. Considering the biological activity of monensin, i.e., the capture and transport of cations across cell membranes, an open and closed form of monensin have been postulated. The identification of these hinge regions, which are only observed in the membrane-like environment of the detergent micelles, provides insight into the mechanism of action and can serve as targets for modification to alter the biological profile of monensin. © 1997 John Wiley & Sons, Inc. Biopoly 42: 759-769, 1997
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    Vancomycin: Interactions with a model cell membrane (1997)
    New York : Wiley-Blackwell
    Biopolymers 42 (1997), S. 627-632 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: No abstract.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    Conformation and dynamics of dimeric ureido-balhimycin (1995)
    New York : Wiley-Blackwell
    Biopolymers 36 (1995), S. 429-437 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The conformation of the antibiotic ureido-balhimycin has been investigated by proton nmr and refined with computer simulations. The dimeric structure cj ureido-balhimycin was established by unambiguous identification of 6 nuclear Overhauser effects (NOEs) as intermonomeric, out of the total of 186 NOEs observed. Via distance geometry calculations the antiparallel orientation of the two monomers was demonstrated. Further refinement by molecular dynamics simulations provided the essential hydrogen bonds and aromatic interactions responsible for interfacial stabilization. The computational protocol illustrated here (distance geometry to define the coarse topology and molecular dynamics for refinement) should find general applicability in the study of homodimers. © 1995 John Wiley & Sons, Inc.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360360406
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  • 10
    Electronic Resource
    Electronic Resource
    Structure of two microcystins: Refinement with nuclear overhauser effects and ensemble calculations (1995)
    New York : Wiley-Blackwell
    Biopolymers 36 (1995), S. 811-828 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Ensemble calculations employing restraints developed from 1H-nmr were used to examine the conformational states of the two microcystins LR and LY. Despite the fast “flip-flop” dynamics about the N-methyl-dehydroalanine residue and adjacent residues, the main conformational characteristics of the cyclic heptapeptides consist of a compact ring formed by five of the seven amino acid residues with expulsion of a dipeptide portion out of the plane and the unnatural C20 β-amino acid (2S. 3S. 8S, 9S)-3-amino-9-methoxy-2, 6, 8-trimethyl-10-phenyldeca-4. 6-dienoic acid pointing upward from the ring. This structure of microcystin LR shows high degrees of similarity with the energy-minimized structure of nodularin, a cyclic pentapeptide of identical inhibitory potency against protein phosphatases 1 and 2A. Comparison of these structures with those of the less toxic LY variant and with the structurally unrelated okadaic acid, known as potent inhibitor of the protein phosphatases 1 and 2A, allowed us to propose a rational binding mode of this structural diverse set of natural inhibitors. © 1995 John Wiley & Sons, Inc.
    Additional Material: 12 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360360613
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