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  • 1
    ISSN: 0887-3585
    Keywords: NMR ; iron-sulfur proteins ; nuclear Overhauser effect ; paramagnetic relaxation ; relaxation matrix analysis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We have accounted for the effect of paramagnetism on the intensities of NOEs in a 73-residue paramagnetic metalloprotein, the reduced high-potential iron sulfur protein ISO I from Ectothiorhodospira halophila, whose solution structure had been recently solved by us. The paramagnetic effects were dealt with through a suitably modified complete relaxation matrix approach. We have then recalculated the structure through a distance geometry program by minimizing the difference between the sixth roots of the calculated and experimental NOEs.The average RMSD, calculated on residues 4-71, within the structures constituting the two families decreased from 0.67 to 0.46 Å for backbone atoms and from 1.23 to 1.06 Å for all heavy atoms. The structures in the new family are for the most part within the indetermination of the previous, less resolved, family. A few specific differences are detected and related to the presence of non-negligible paramagnetic effects, which are now properly evaluated.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 348-358 
    ISSN: 0887-3585
    Keywords: ferredoxin ; NMR ; paramagnetic ; relaxation ; solution structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The possibility of using the relaxation properties of nuclei for solution structure determination of paramagnetic metalloproteins is critically evaluated. First of all, it is theoretically and experimentally demonstrated that magnetization recovery in non-selective inversion recovery experiments can be approximated to an exponential in both diamagnetic and paramagnetic systems. This permits the estimate of the contribution of paramagnetic relaxation when dominant or sizable. Then, it is shown that the averaging of paramagnetic relaxation rates due to cross relaxation is often tolerably small with respect to the use of paramagnetic relaxation rates as constraints for structural determination. Finally, a protocol is proposed to use such paramagnetic relaxation rates, which depend on the sixth power of the metal to resonating nucleus distance, as constraints for solution structure determination of proteins. As an example, the available solution structure of the oxidized ferredoxin from Clostridium pasteurianum has been significantly improved in resolution especially in the proximity of the metal ions by using 69 new constraints based on paramagnetic relaxation. Proteins 29:348-358, 1997. © 1997 Wiley-Liss, Inc.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
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  • 3
    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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  • 4
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 186-197 
    ISSN: 0887-3585
    Keywords: carboxypeptidas ; molecular dynamics ; enzymatic mechanisms ; peptidase mechanism ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: An MD simulation of the system carboxypeptidase A (CPA) with the tetrapeptide Val-Leu-Phe-Phe has been performed in order to learn about the substrate disposition just prior to nucleophilic attack. We have explored the model in which the substrate does not substitute the zinc-coordinated water (the “water” mechanism). The simulations do suggest as feasible that the Zn-OH2 group performs a nucleophilic attack on the Phe-Phe peptidic bond. We have also investigated the model in which the carbonyl oxygen displaces the zinc-coordinated water. In this case the substrate and Glu-270 orient themselves to allow an anhydride intermediate during the peptidic bond cleavage (the “anhydride” mechanism). Based on the results of the simulations, both “water” and “anhydride” mechanisms are structurally feasible, although the former model seems more probable on chemical grounds. © 1994 John Wiley & Sons, Inc.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    Weinheim : Wiley-Blackwell
    Berichte der deutschen chemischen Gesellschaft 1998 (1998), S. 583-591 
    ISSN: 1434-1948
    Keywords: Cytochrome c ; Hyperfine shift ; Magnetic susceptibility anisotropy ; NMR spectroscopy ; Heme proteins ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The binding of ammonia to oxidized horse heart cytochrome c has been studied by 1H-NMR, EPR, and CD spectroscopy at pH = 8.0. The affinity constant of the ligand is in the range 1.5-4 M-1. The 1H-NMR spectra of the heme group have been found to be similar to those of the high-pH forms, high-temperature forms, and cyanide adduct of the Met80Ala mutant of S. cerevisiae iso-1-cytochrome c. The assignment of a number of signals has led to the determination of the values of the magnetic anisotropy and of the orientation of its axes. The latter are similar to those of the Met80Ala cyanide derivative. The assignment of the high-temperature species has been further pursued during this research. The analysis of the NMR data of the NH3 adduct leads to the conclusion that substitution of Met80 at high pH or high temperature occurs through a ligand with cylindrical symmetry. This supports the suggestion that Met80 is substituted by a lysine at high pH.
    Type of Medium: Electronic Resource
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  • 6
    ISSN: 1434-1948
    Keywords: NMRD ; MRI ; Contrast agents ; Carbonic anhydrase ; Sulfonamides ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A novel Gd-DTPA derivative with a built-in sulfonamide (SA) was synthesized as a contrast agent for MRI. The complex was designed to selectively target the enzyme carbonic anhydrase. It is shown that the longitudinal relaxation rates of aqueous solutions of Gd-DTPA-SA in the presence of carbonic anhydrase increase significantly. The binding constant is determined to be 15,000 ± 5,000 M-1. This value ensures substantial formation of the carbonic anhydrase adduct at imaging concentrations of Gd-DTPA-SA. The complex interacts with erythrocytes, presumably due to a high affinity for the carbonic anhydrase present on the outer surface of the latter. This takes place even though the enzyme has a low abundance and is easily saturated by small amounts of Gd-DTPA-SA. The interaction of Gd-DTPA-SA with serum proteins is negligibly small. Therefore, the complex could potentially be tested as a selective contrast agent for compartments outside the blood pool.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
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  • 7
    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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  • 8
    Electronic Resource
    Electronic Resource
    Chichester : Wiley-Blackwell
    Organic Magnetic Resonance 31 (1993), S. S1 
    ISSN: 0749-1581
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 9
    ISSN: 0749-1581
    Keywords: 1H NMR ; Copper-cobalt dismutase ; 1D-NOESY ; 2D-NOESY ; T1 measurements ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Through 1D and 2D NOESY experiments, samples of copper-cobalt superoxide dismutase in which the histidines had been completely deuteriated except for the β-CH2 protons were investigated. In this way a simplified spectrum was obtained which allowed the detection of the His NHs of the cobalt domain and their assignment through the kinetics of the proton-deuterium exchange. Further, the β-CH2 protons of Asp 83 were stereospecifically assigned through T1 measurements. Some backbone protons were also assigned.
    Additional Material: 4 Ill.
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