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  • 1
    ISSN: 1573-5001
    Keywords: paramagnetic metalloproteins ; pseudocontact shifts ; solution structures ; structure refinement
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract The program DYANA, for calculation of solution structures of biomolecules with an algorithm based on simulated annealing by torsion angle dynamics, has been supplemented with a new routine, PSEUDYANA, that enables efficient use of pseudocontact shifts as additional constraints in structure calculations of paramagnetic metalloproteins. PSEUDYANA can determine the location of the metal ion inside the protein frame and allows to define a single tensor of magnetic susceptibility from a family of conformers. As an illustration, a PSEUDYANA structure calculation is provided for a metal-undecapeptide complex, where simulated pseudocontact shifts but no NOE restraints are used as conformational constraints.
    Type of Medium: Electronic Resource
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  • 2
    ISSN: 0887-3585
    Keywords: pseudocontact shifts ; structure calculations ; restrained energy minimization ; molecular dynamics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The pseudocontact shifts of NMR signals, which arise from the magnetic susceptibility anisotropy of paramagnetic molecules, have been used as structural constraints under the form of a pseudopotential in the SANDER module of the AMBER 4.1 molecular dynamics software package. With this procedure, restrained energy minimization (REM) and restrained molecular dynamics (RMD) calculations can be performed on structural models by using pseudocontact shifts. The structure of the cyanide adduct of the Met80Ala mutant of the yeast iso-1-cytochrome c has been used for successfully testing the calculations. For this protein, a family of structures is available, which was obtained by using NOE and pseudocontact shifts as constraints in a distance geometry program. The structures obtained by REM and RMD calculations with the inclusion of pseudocontact shifts are analyzed. Proteins 29:68-76, 1997. © 1997 Wiley-Liss, Inc.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
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  • 3
    ISSN: 0947-6539
    Keywords: electron transfer ; iron-sulfur proteins ; NMR spectroscopy ; proteins ; solution structures ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In the 1H NMR spectrum of the oxidized form of the high-potential iron-sulfur protein (HiPIPI) from Ectothiorhodospira halophila, 91% of the total proton resonances and 100% of the residues have been assigned. The standard COSY, NOESY, and TOCSY sequences have been optimized for the paramagnetism of the molecule. Extensive assignment of the 15N NMR spectrum has been obtained through HMQC spectra. With 1437 dipolar connectivities, of which about 10% involved fast-relaxing protons, a family of 18 structures was generated with an RMSD of 0.65 Å by using the programs developed by Wüthrich. The family of structures was further refined by various calculation steps; the final RMSD was 0.48 Å. The structures appear to be very similar but not equal to the structures of the reduced protein. Despite the similarity in structure, significant variations in the chemical shifts are observed. A similar behavior was observed for the homologous protein from Chromatium vinosum. It is concluded that NMR is a sensitive tool to monitor differences between oxidized and reduced proteins; however, the detailed structural variations should be evaluated with caution at the present level of resolution, which roughly corresponds to a resolution of 2.5 Å in an X-ray structure.
    Additional Material: 12 Ill.
    Type of Medium: Electronic Resource
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