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  • 1
    Electronic Resource
    Electronic Resource
    Evaluation of errors of interproton distances and correlation time determined from NMR cross-relaxation rates (1992)
    Springer
    Journal of biomolecular NMR 2 (1992), S. 573-582 
    Details
    ISSN: 1573-5001
    Keywords: Amaninamide ; Correlation time ; Evaluation of errors ; Interproton distances ; NOESY ; ROESY ; 2D NMR ; Peptides ; Cross-relaxation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Summary We have analyzed a combined use of the two-dimensional nuclear Overhauser effect in the laboratory frame (NOESY) and in the rotating frame (ROESY) to determine interproton distances and correlation time in medium-sized rigid molecules (Davis, 1987). This method can be applied in the intermediate motional regime, 0.2 〈 ωoτc, 〈 5, (τc, correlation time, (ωo resonance frequency). Error limits depend on the motional regime and are smallest near ωoτc=1.14. The method was tested on six geminal proton pairs in the bicyclic octapeptide (S-deoxo-γ-[R]-OH-Ile3 amaninamide, Mw =870) for which at 297 K in DMSO, a correlation time of 1.0 ns, with a standard deviation of 0.12 ns, and an interproton distance of 1.87 Å, with standard deviation of 0.04 Å, are obtained.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02192846
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  • 2
    Electronic Resource
    Electronic Resource
    Simulated dipeptide recognition by vancomycin (1997)
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 10 (1997), S. 73-87 
    Details
    ISSN: 0952-3499
    Keywords: glycopeptide antibiotics ; free energy perturbation ; molecular dynamics simulation ; molecular recognition ; computer-assisted drug design ; 2D NMR ; simulated annealing ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The antimicrobial activity of vancomycin and related glycopeptide antibiotics is due to stereospecific recognition of polypeptide components in bacterial cell walls. To better understand how these antibiotics recognize polypeptide determinants, we have developed dynamic models of the complexes formed by the vancomycin aglycon and two different dipeptide ligands, Ac-D-ala-D-ala and Ac-D-ala-gly. Molecular dynamics simulations of the two complexes, initially conditioned with distance constraints derived from two-dimensional nuclear magnetic resonance (NMR) studies, are conformationally stable and propagate in a manner consistent with the NMR-derived constraints after the constraints are removed. Free energy calculations accurately predict the relative binding affinity of these two complexes and help validate the simulation models for detailed structural analysis. Although the two ligands adopt similar conformations when bound to the antibiotic, there are clear differences in the configuration of intermolecular hydrogen bonds, the overall shape of the antibiotic, and other structural features of the two complexes. This analysis illustrates how complex structural and dynamic factors interrelate and contribute to differences in binding affinity. © 1997 John Wiley & Sons, Ltd.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
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    Paper (German National Licenses)
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