Thermodynamic and kinetic modelling of the redox properties of tetrahaem cytochromes C3

Dissertação apresentada para obtenção do grau de Doutor em Bioquímica,especialidade Bioquímica-Física, pela Universidade Nova de Lisboa, Faculdade de Cincias e TecnologiaThe work presented in this thesis concerns the description and modelling of the thermodynamic and kinetic properties of tetrahaem cytochromes C3 isolated from different Desulfovibrio spp.. Sulfate-reducing bacteria produce tetrahaem cytochrome C3 in large quantities. This small (13 - 15 kD) protein is located in the periplasmic space of the cells,where it has been proposed to work as a cofactor of the enzyme hydrogenase. The four haems in cytochrome C3 are covalently bound to the protein through thioether linkages with cysteinyl residues and all display bis-histidinyl axial coordination. Although the degree of homology between the amino acid sequence of cytochromes C3 isolated from different organisms is low, the architecture of the haem core, is strictly conserved. The modelling of the thermodynamic properties of this protein has to take into account the fact that the four haems display different, interacting, and pH dependent redox potentials. Various approaches are described and discussed in this thesis, giving special emphasis to models which include both haem-haem and haem-proton interactions. To explain the pH dependence of the NMR resonances, the acid/base (NB) model was developed under the assumption that the protein could undergo a proton-linked conformational change, each conformation being characterised by a different set of microscopic redox potentials and haemhaem interacting potentials. The model of five interacting centres, developed later, demonstrated that it is not necessary to make any structural assumptions and that the experimental data can be simulated using fewer parameters, which are therefore better defined. According to this model, the thermodynamic properties of cytochrome C3 can be described by the intrinsic microscopic parameters of one acid/base and four redox centres plus the two-site interactions established between the five centres, namely, six haem-haem interactions plus four haem-proton interactions. Application of this model to NMR and visible redox titrations enabled the accurate determination of the complete set of microscopic parameters that characterise the thermodynamic behaviour of cytochromes C3 isolated from D. gigas and D. vulgaris. It is apparent from the values of the thermodynamic parameters that these cytochromes are able to perform a concerted two-electron step, which is coupled to the simultaneous uptake or release of protons, depending on the direction of the electron flow. These properties allow cytochrome C3 to work as an energy transducing system. However, since kinetic control of the electron and proton transfer steps is essential to achieve energy transduction, the kinetic properties of cytochrome C3 isolated from D. gigas are described and analysed in the second half of this thesis, making use of a specially developed kinetic model