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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
    Redox-Bohr effect in the tetrahaem cytochrome c3 from Desulfovibrio vulgaris: a model for energy transduction mechanisms (1996)
    Springer
    JBIC 1 (1996), S. 34-38 
    Details
    ISSN: 1432-1327
    Keywords: Key words Cytochrome c3 ; Hydrogenase ; Energy transduction ; Electron transfer mechanism ; Redox-Bohr
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract  Using potentiometric titrations, two protons were found to participate in the redox-Bohr effect observed for cytochrome c 3 from Desulfovibrio vulgaris (Hildenborough). Within the framework of the thermodynamic model previously presented, this finding supports the occurrence of a concerted proton-assisted 2e– step, ideally suited for the coupling role of cytochrome c 3 to hydrogenase. Furthermore, at physiological pH, it is shown that when sulfate-reducing bacteria use H2 as energy source, cytochrome c 3 can be used as a charge separation device, achieving energy transduction by energising protons which can be left in the acidic periplasmic side and transferring deenergised electrons to sulfate respiration. This mechanism for energy transduction, using a full thermodynamic data set, is compared to that put forward to explain the proton-pumping function of cytochrome c oxidase.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s007750050020
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    Paper (German National Licenses)
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  • 3
    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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  • 4
    Electronic Resource
    Electronic Resource
    Redox-Bohr effect in electron/proton energy transduction: cytochrome c 3 coupled to hydrogenase works as a 'proton thruster' in Desulfovibrio vulgaris (1997)
    Springer
    JBIC 2 (1997), S. 488-491 
    Details
    ISSN: 1432-1327
    Keywords: Key words Cytochrome c3 ; Electron transfer ; Proton transfer ; Redox-Bohr ; Energy transduction
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract  A central step in the metabolism of Desulfovibrio spp. is the oxidation of molecular hydrogen catalyzed by a periplasmic hydrogenase. However, this enzymatic activity is quite low at physiological pH. The hypothesis that, in the presence of the tetrahaem cytochrome c 3, hydrogenase can maintain full activity at physiological pH through the concerted capture of the resulting electrons and protons by the cytochrome was tested for the case of Desulfovibrio vulgaris (Hildenborough). The crucial step involves an electron-to-proton energy transduction, and is achieved through a network of cooperativities between redox and ionizable centers within the cytochrome (redox-Bohr effect). This mechanism, which requires a relocation of the proposed proton channel in the hydrogenase structure, is similar to that proposed for the transmembrane proton pumps, and is the first example which shows evidence of functional energy transduction in the absence of a membrane confinement.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s007750050160
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    Paper (German National Licenses)
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  • 5
    Electronic Resource
    Electronic Resource
    Structural and magnetic characterisation of the haem core of ferricytochromes c 6 (1998)
    Springer
    JBIC 3 (1998), S. 68-73 
    Details
    ISSN: 1432-1327
    Keywords: Key words Cytochrome c6 ; His-Met coordination ; Photosynthesis ; 1H and13C paramagnetic NMR ; Dipolar field
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract  NMR studies of the paramagnetic 13C shifts of haem substituents in ferricytochromes c 6 from Monoraphidium braunii and Anabaena sp. PCC7119 were used to explore the unusual electronic structure of these two proteins and to describe the functional centre of the latter, for which there is still no other structural information. Even without evaluating the contribution of the dipolar shifts to the paramagnetic 13C shift of the haem substituents, a good description of the rhombic perturbation is obtained, which gives a measure of the spatial arrangement of the axial ligands of the iron as well as a preliminary characterisation of the magnetic properties of the unpaired electron. If complemented by EPR data, the dipolar field can be fully described and is a valuable aid for the assignment of NMR spectra, providing direct information on the solution structure in the oxidised state. In contrast to the great difference in the primary structure of the two cytochromes c 6 studied, the results show close similarity between their haem cores, suggesting that this structural arrangement may have been selectively produced by nature to perform a specific electron transfer task, and that the variability in amino-acid sequence is determined by the requirements of recognition of the physiological partners.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s007750050208
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  • 6
    Electronic Resource
    Electronic Resource
    Comparative redox and pK a calculations on cytochrome c 3 from several Desulfovibrio species using continuum electrostatic methods (1999)
    Springer
    JBIC 4 (1999), S. 73-86 
    Details
    ISSN: 1432-1327
    Keywords: Key words Protein electrostatistics ; Electron-proton coupling ; Redox-Bohr effect ; pKa calculations ; Cytochrome c3
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract  A comparative study of the pH-dependent redox mechanisms of several members of the cytochrome c 3 family has been carried out. In a previous work, the molecular determinants of this dependency (the so-called redox-Bohr effect) were investigated for one species using continuum electrostatic methods to find groups with a titrating range and strength of interaction compatible with a mediating role in the redox-Bohr effect. Here we clarify these aspects in the light of new and improved pK a calculations, our findings supporting the hypothesis of propionate D from heme I being the main effector in the pH-dependent modulation of the cytochrome c 3 redox potentials in all the c 3 molecules studied here. However, the weaker (but significant) role of other titrating groups cannot be excluded, their importance and identity changing with the particular molecule under study. We also calculate the relative redox potentials of the four heme centers among the selected members of the c 3 family, using a continuum electrostatic method that takes into account both solvation and interaction effects. Comparison of the calculated values with available data for the microscopic redox potentials was undertaken, the quality of the agreement being dependent upon the choice of the dielectric constant for the protein interior. We find that high dielectric constants give best correlations, while low values result in better magnitudes for the calculated potentials. The possibility that the crystallographic calcium ion in c 3 from Desulfovibrio gigas may be present in the solution structure was tested, and found to be likely.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s007750050291
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