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  • 1
    Electronic Resource
    Electronic Resource
    Determination of solution structures of paramagnetic proteins by NMR (1998)
    Springer
    European biophysics journal 27 (1998), S. 367-375 
    Details
    ISSN: 1432-1017
    Keywords: Key words Paramagnetic proteins ; Cytochromes ; Solution structure ; NMR ; Dipolar interactions ; Magnetic properties
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Physics
    Notes: Abstract Standard procedures for using nuclear Overhauser enhancements (NOE) between protons to generate structures for diamagnetic proteins in solution from NMR data may be supplemented by using dipolar shifts if the protein is paramagnetic. This is advantageous since the electron-nuclear dipolar coupling provides relatively long-range geometric information with respect to the paramagnetic centre which complements the short-range distance constraints from NOEs. Several different strategies have been developed to date, but none of these attempts to combine data from NOEs and dipolar shifts in the initial stages of structure calculation or to determine three dimensional protein structures together with their magnetic properties. This work shows that the magnetic and atomic structures are highly correlated and that it is important to have additional constraints both to provide starting parameters for the magnetic properties and to improve the definition of the best fit. Useful parameters can be obtained for haem proteins from Fermi contact shifts; this approach is compared with a new method based on the analysis of dipolar shifts in haem methyl groups with respect to data from horse and tuna ferricytochromes c. The methods developed for using data from NOEs and dipolar shifts have been incorporated in a new computer program, PARADYANA, which is demonstrated in application to a model data set for the sequence of the haem octapeptide known as microperoxidase-8.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002490050144
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  • 2
    Electronic Resource
    Electronic Resource
    Site-directed mutagenesis of a phenylalanine residue strictly conserved in cytochromes c 3 (1996)
    Springer
    JBIC 1 (1996), S. 542-550 
    Details
    ISSN: 1432-1327
    Keywords: Key words Cytochrome c3 ; Mutagenesis ; Redox-Bohr ; NMR ; EPR ; Cooperativity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract  Reduction of the haems in tetrahaem cytochromes c 3 is a cooperative process, i.e., reduction of each of the haems depends on the redox states of the other haems. Furthermore, electron transfer is coupled to proton transfer (redox-Bohr effect). Two of its haems and a strictly conserved nearby phenylalanine residue, F20, in Desulfovibrio vulgaris (Hildenborough) cytochrome c 3 form a structural motif that is present in all cytochromes c 3 and also in cytochrome c oxidase. A putative role for this phenylalanine residue in the cooperativity of haem reduction was investigated. Therefore, this phenylalanine was replaced, with genetic techniques, by isoleucine and tyrosine in D. vulgaris (Hildenborough) cytochrome c 3. Cyclic voltammetry studies revealed a small increase (30 mV) in one of the macroscopic redox potentials in the mutated cytochromes. EPR showed that the main alterations occurred in the vicinity of haem I, the haem closest to residue 20 and one of the haems responsible for positive cooperativities in electron transfer of D. vulgaris cytochrome c 3. NMR studies of F20I cytochrome c 3 demonstrated that the haem core architecture is maintained and that the more affected haem proton groups are those near the mutation site. NMR redox titrations of this mutated protein gave evidence for only small changes in the relative redox potentials of the haems. However, electron/electron and proton/electron cooperativity are maintained, indicating that this aromatic residue has no essential role in these processes. Furthermore, chemical modification of the N-terminal amino group of cytochrome c 3 backbone, which is also very close to haem I, had no effect on the network of cooperativities.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s007750050090
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  • 3
    Electronic Resource
    Electronic Resource
    Reevaluation of the redox and redox-Bohr cooperativity in tetrahaem Desulfovibrio vulgaris (Miyazaki F) cytochrome c 3 (1997)
    Springer
    JBIC 2 (1997), S. 343-349 
    Details
    ISSN: 1432-1327
    Keywords: Key words Cooperativity ; Cytochrome c3 ; NMR ; Paramagnetic ; Redox-Bohr
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract  The thermodynamic model of five interacting charge centres (four haems and an ionisable centre), which was used in the characterisation of the thermodynamic properties of Desulfovibrio vulgaris (Hildenborough) cytochrome c 3 (c 3DvH), is now used to reevaluate the thermodynamic properties in Desulfovibrio vulgaris (Miyazaki F) cytochrome c 3 (c 3DvM) on the basis of published data (Park, J.-S., Ohmura, T., Kano, K., Sagara, T., Niki, K., Kyogoku, Y. and Akutsu, H. (1996) Biochim. Biophys. Acta 1293, 45–54). Contrary to the assertion of Park et al. (1996), the pH dependence of the proton chemical shifts of haem methyls in c 3DvM in several stages of oxidation is well described by the model, which involves both homotropic (e–/e–) and heterotropic (e–/H+) cooperativity. This shows that the pH dependence observed for c 3DvM is not significantly more complicated than that observed for c 3DvH. Since the parameters which we now obtain for c 3DvM are generated with the same model as those from c 3DvH, albeit using less precise data, it is possible to make a preliminary comparison of the thermodynamic properties of these two proteins and of their role in energy transduction. The extrinsic dipolar shifts generated for each methyl group by each of the four haems in c 3DvM are also determined. A novel method for approximating the magnetic susceptibility tensors is used: the orientations of the principal axes of the tensors have been shown to be closely related to the geometry of the axial ligands, which is available from the X-ray structure of c 3DvM, and the components of the tensors are extrapolated from EPR g values. The inclusion of the calculated haem extrinsic contributions clearly describes the pH dependence of the haem methyls in the core of the protein, close to other haems. This description is most remarkable in the case of the haem methyl 21CH3 II I, for which the "unusual pH dependence" commented on by Park et al. (1996) is easily explained using the thermodynamic parameters determined by our model together with the calculated extrinsic dipolar shifts, thus providing a test of the analysis.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s007750050141
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  • 4
    Electronic Resource
    Electronic Resource
    Structure of the three-haem core of cytochrome c 551.5 determined by 1H NMR (1996)
    Springer
    JBIC 1 (1996), S. 305-311 
    Details
    ISSN: 1432-1327
    Keywords: Key words Multihaem cytochromes ; Cytochrome c551.5 ; Cytochrome c3 ; Sulfate-reducing bacteria ; NMR
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract  The trihaem cytochrome c 551.5, formerly known as cytochrome c 7, from the organism Desulfuromonas acetoxidans, has been studied in the reduced state by 2D proton NMR. The haem proton resonances were assigned, and several nuclear Overhauser enhancements (NOEs) between resonances arising from different haems were detected and assigned. The relative orientations of the three haems were calculated by fitting both the intensities of the interhaem NOEs and the magnitudes of the ring current shifts of the haem resonances, following the strategy previously used by the authors to reassess the X-ray structure of the haem core in tetrahaem cytochrome c 3 from Desulfumicrobium baculatum. It is concluded that, although the comparison of the protein sequence with those of the tetrahaem cytochromes c 3 shows that in cytochrome c 551.5 about 40% of the sequence is deleted, including the region involved in the attachment of the second of the four haems, this does not induce any significant rearrangement of the remaining three haems other than a slight decrease in the iron-iron distance between two of the haems, namely those corresponding to haems I and IV of cytochrome c 3.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s007750050058
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  • 5
    Electronic Resource
    Electronic Resource
    Characterization of cytochrome c 6 from the cyanobacterium Anabaena PCC 7119 (1997)
    Springer
    JBIC 2 (1997), S. 225-234 
    Details
    ISSN: 1432-1327
    Keywords: Key words Cytochrome c6 ; Anabaena PCC 7119 ; EPR ; NMR ; Redox-Bohr
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract  A soluble monoheme c–type cytochrome c 6 has been isolated from the cyanobacterium Anabaena PCC 7119. It is a basic protein, with a molecular mass of 9.7 kDa, which accepts electrons from Anabaena ferredoxin in the ferredoxin-NADP+reductase-dependent NADPH cytochrome c reductase activity assay. The turnover of the reaction has an optimum pH at 7.5. Flavodoxin can also replace ferredoxin in this assay, but with only 20% efficiency. Plastocyanin from Anabaena PCC 7119, as well as the c 6 cytochromes from the green algae Chlorella fusca and Monoraphidium braunii are also shown to accept electrons from Anabaena ferredoxin. The reduction potential of cytochrome c 6 at pH 6.7 was determined to be 338 mV and is pH dependent, with pK a ox=8.4±0.1 and pK a red≈9.5. The ferric and ferrous cytochrome forms and their pH equilibria have been studied using visible, EPR and 1H-NMR spectroscopies. The amino acid sequence and the visible and NMR spectroscopic data indicate that the heme iron has a methionine-histidine axial coordination in the pH range 5–11. However, the EPR data for the ferricytochrome are complex and show that in this pH range five distinct forms are present. Between pH 5 and 9 the spectrum is dominated by two rhombic species, with g–values at 2.94, 2.29, 1.43 and at 2.84, 2.34, 1.56, which interconvert with a pK a of 8.4. The NMR data also show a main interconversion between two cytochrome forms at this pH, which coincides with that determined from the pH dependence of the reduction potential. Both these forms were associated with a methionine-histidine heme-iron coordination by correlation with the visible and NMR spectral data, although having crystal field parameters atypical for this type of coordination. Anabaena cytochrome c 6 is one more example of a heme protein for which the widely used crystal field analysis of the EPR data (truth diagram) fails to unequivocally determine the type of heme-iron ligation.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s007750050128
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