Poisson-Boltzmann (PB) models are a fast and common tool for studying electrostatic processes in proteins, particularly their ionization equilibrium (protonation and/or reduction), often yielding quite good results when compared with more detailed models. Yet, they are conceptually very simple and necessarily approximate, their empirical character being most evident when it comes to the choice of the dielectric constant assigned to the protein region. The present study analyzes several factors affecting the ability of PB-based methods to model protein ionization equilibrium. We give particular attention to a suggestion made by Warshel and co-workers (e.g., Sham et al. J. Phys. Chem. B 1997, 101, 4458) of using different protein dielectric constants for computing the individual (site) and the pairwise (site-site) terms of the ionization free energies. Our prediction of pK(a) values for several proteins indicates that no advantage is obtained by such a procedure, even for sites that are buried and/or display large pK(a) shifts relative to the solution values. In particular, the present methodology gives the best predictions using a dielectric constant around 20, for shifted/buried and nonshifted/exposed sites alike. The similarities and differences between the PB model and Warshel's PDLD/S model are discussed, as well as the reasons behind their apparently discrepant results. The present PB model is shown to predict also good reduction potentials in redox proteins.

The gene encoding cytochrome c nitrite reductase (NrfA) from Desulfovibrio desulfuricans ATCC 27774 was sequenced and the crystal structure of the enzyme was determined to 2.3-A resolution. In comparison with homologous structures, it presents structural differences mainly located at the regions surrounding the putative substrate inlet and product outlet, and includes a well defined second calcium site with octahedral geometry, coordinated to propionates of hemes 3 and 4, and caged by a loop non-existent in the previous structures. The highly negative electrostatic potential in the environment around hemes 3 and 4 suggests that the main role of this calcium ion may not be electrostatic but structural, namely in the stabilization of the conformation of the additional loop that cages it and influences the solvent accessibility of heme 4. The NrfA active site is similar to that of peroxidases with a nearby calcium site at the heme distal side nearly in the same location as occurs in the class II and class III peroxidases. This fact suggests that the calcium ion at the distal side of the active site in the NrfA enzymes may have a similar physiological role to that reported for the peroxidases.

The cytochrome c nitrite reductase is isolated from the membranes of the sulfate‐reducing bacterium Desulfovibrio desulfuricans ATCC 27774 as a heterooligomeric complex composed by two subunits (61 kDa and 19 kDa) containing c‐type hemes, encoded by the genes nrfA and nrfH, respectively. The extracted complex has in average a 2NrfA:1NrfH composition. The separation of ccNiR subunits from one another is accomplished by gel filtration chromatography in the presence of SDS. The amino‐acid sequence and biochemical subunits characterization show that NrfA contains five hemes and NrfH four hemes. These considerations enabled the revision of a vast amount of existing spectroscopic data on the NrfHA complex that was not originally well interpreted due to the lack of knowledge on the heme content and the oligomeric enzyme status. Based on EPR and Mössbauer parameters and their correlation to structural information recently obtained from X‐ray crystallography on the NrfA structure [Cunha, C.A., Macieira, S., Dias, J.M., Almeida, M.G., Gonçalves, L.M.L., Costa, C., Lampreia, J., Huber, R., Moura, J.J.G., Moura, I. & Romão, M. (2003) J. Biol. Chem. 278, 17455–17465], we propose the full assignment of midpoint reduction potentials values to the individual hemes. NrfA contains the high‐spin catalytic site (−80 mV) as well as a quite unusual high reduction potential (+150 mV)/low‐spin bis‐His coordinated heme, considered to be the site where electrons enter. In addition, the reassessment of the spectroscopic data allowed the first partial spectroscopic characterization of the NrfH subunit. The four NrfH hemes are all in a low‐spin state (S = 1/2). One of them has a gmax at 3.55, characteristic of bis‐histidinyl iron ligands in a noncoplanar arrangement, and has a positive reduction potential.

Political communication has transformed drastically since the Internet made its way into the political arena. Political parties seem unable to do without a website or a social networking profile any longer, particularly in election campaigns. One of the many approaches to studying online political communication is measuring specific website features political parties, politicians and candidates utilize in order to engage visitors in the political process. Even though the analysis of online political communication has evolved over the years, website-feature analysis is still a valid instrument to study political actors. The explanations sought to understand website-feature utilization are found in earlier cross-national comparative studies (technological and human development) as well as new ones (political systems characteristics, ideology, participation and engagement). This study looks back on two prior cross-national comparative research projects and reports on a cross-national comparative analysis of 1026 candidate and party websites from 17 countries participating in the European Parliament (EP) elections of 2009. To analyze these data, some methodological improvements are made compared to earlier studies.

Theoretical studies of protein-protein association and electron transfer were performed on the binary systems formed by Desulfovibrio vulgaris Hildenborough (D. v. H.) flavodoxin and D. v. H. cytochrome c553 and by flavodoxin and horse heart cytochrome c. Initial structures for the complexes were obtained by rigid-body docking and were refined by MD to allow for molecular flexibility. The structures thus obtained were analysed in terms of their relative stability through the calculation of excess energies. Electrostatic, van der Waals and solvation energy terms showed all to have significant contributions to the stability of complexes. In the best association solutions found for both cytochromes, these bind to different zones of flavodoxin. The binding site of flavodoxin observed for cytochrome c is in accordance with earlier works [27]. The various association modes found were characterised in terms of electron transfer using the Pathways model. For complexes between flavodoxin and horse heart cytochrome c, some correlation was observed between electron tunnelling coupling factors and conformation energy; the best conformation found for electron transfer corresponded also to the best one in terms of energy. For complexes between flavodoxin and cytochrome c553 this was not the case and a lower correlation was observed between electron tunnelling coupling factors and excess energies. These results are in accordance with the differences in the experimental dependence of electron transfer rates with ionic strength observed between these two cases.

A hypothetical model for the non-physiological electron transfer complex between cytochrome c553 (c553) and the flavodoxin (fld) from the sulphate-reducing bacteria Desulfovibrio vulgaris has been recently published [1] based on rigid-body docking and refined by molecular dynamics. In this study, the functional validity of this model is tested by looking at the role of electrostatics in the non-physiological interprotein electron transfer between the two proteins at different ionic strengths. The results are compared with the electron transfer between fld and cytochrome c from horse heart (hhc). Second-order rate constants (k2) were measured for both non-physiological systems at different ionic strengths: a complex, bell-shaped behaviour is observed for the k2 of the c553/fld redox pair with an optimum rate at I=58 mmol l(-1), whereas under the same conditions the k2 for hhc/fld decreased monotonically with increasing ionic strength. Results from the electron transfer kinetics are rationalised in terms of reorganisational effects of an ensemble of conformations of the electron transfer competent c553/fld complexes, consistent with the published model.

The analysis in this article focuses on the vertical and horizontal communication patterns of MPs, drawing on examples from a comparative survey done in seven European countries. The results show that the MPs in these countries can still be said to be in an initial phase of exploiting the full range of these new technologies to support their parliamentary and partisan activity, and that traditional media such as television, radio and newspapers are still the favoured means for political communication. In so far as ICT is used, MPs primarily use these means for internal communication within the party or within parliament, and not very much for external communication with constituents, journalists, lobbyists, etc. Analysing the use of homepages and political campaign via ICT both of these means are seen to be largely dependent on the political party of the MP, and the partyfls electoral strategies, limiting individual initiatives by MPs. Also, a certain disinterest in a more extensive us e of ICT on the part of the MPs was found. There seem to be a number of reasons for this disinterest, among these the argument that there is still a considerable digital divide especially in the Southern European countries. However, as computer and Internet diffusion continues to increase rapidly this argument becomes increasingly invalid.

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