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  • 1985-1989  (2)
  • Computational Chemistry and Molecular Modeling  (2)
  • 1
    Digitale Medien
    Digitale Medien
    A specific inhibitor design approach by means of molecular dynamics calculation for porcine pancreatic elastase (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 645-650 
    Details
    ISSN: 0192-8651
    Schlagwort(e): Computational Chemistry and Molecular Modeling ; Biochemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: A 27-picosecond (ps) molecular dynamics calculation has been carried out for the 1:2 enzyme-ligand complex between porcine pancreatic elastase (PPE) and acetyl-alanine-proline-alanine (APA). A data analysis has been carried out using a total of 450 structures. During the simulation, the root-mean-square fluctuations (RMSF) increased compared with the x-ray data. Some differences of the hydrogen bond arrangement in the MD average structures are found especially for SER 195, suggesting the fluctuations of the ligand molecules. The radius of gyration decreased a little during the simulation. Although intermolecular hydrogen bonds between two substrates (APA1 and APA2) has not been found by a 1.65-Å high-resolution x-ray diffraction study, the MD calculation showed the intermolecular hydrogen bond between them to be 3.2 Å. The extended active site of PPE is so wide compared with the size of a tripeptide that such a hydrogen-bound hexapeptide can be more specific than tripeptides, which is consistent with the kinetic data previously reported.
    Zusätzliches Material: 2 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540080509
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  • 2
    Digitale Medien
    Digitale Medien
    Molecular dynamics simulation of the 1:1 enzyme-ligand complex between porcine pancreatic elastase and acetyl-alanine-proline-alanine (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 801-809 
    Details
    ISSN: 0192-8651
    Schlagwort(e): Computational Chemistry and Molecular Modeling ; Biochemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: A 31.5 picosecond (ps) MD calculation has been completed for the 1:1 enzyme-ligand complex between porcine pancreatic elastase (PPE) and acetyl-alanine-proline-alanine (APA). The 1:2 complex studied crystallographically at product saturation conditions precludes the study of a 1:1 complex (PPE and APA1); this objective has been achieved by computational methods described here. The acetyl group of the ligand was found to occupy two neighboring sites, one within the primary specificity site and the other out into solution. The primary change of the ligand structure is ψ1 torsion angle being 171.5°. Supported by an interactive graphic display, the dynamical fluctuations of a smaller ligand compared with the width of the active site as PPE were observed by the MD simulation, although the complex has not been detected by any spectroscopic method.
    Zusätzliches Material: 2 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540080608
    Bibliothek Standort Signatur Band/Heft/Jahr Verfügbarkeit
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