In eukaryotic cells, most proteins in the cytosol and nucleus are degraded via the ubiquitin-proteasome pathway. The 26S proteasome is a 2.5-MDa molecular machine built from approximately 31 different subunits, which catalyzes protein degradation. It contains a barrel-shaped proteolytic core complex (the 20S proteasome), capped at one or both ends by 19S regulatory complexes, which recognize ubiquitinated proteins. The regulatory complexes are also implicated in unfolding and translocation of ubiquitinated targets into the interior of the 20S complex, where they are degraded to oligopeptides. Structure, assembly and enzymatic mechanism of the 20S complex have been elucidated, but the functional organization of the 19S complex is less well understood. Most subunits of the 19S complex have been identified, however, specific functions have been assigned to only a few. A low-resolution structure of the 26S proteasome has been obtained by electron microscopy, but the precise arrangement of subunits in the 19S complex is unclear.

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Electrophysiology and structural studies were performed on an annexin V variant containing a mutation of glutamic acid-95 to serine in the center of the pore region. The mutation resulted in a lower single channel conductance for calcium and a strongly increased conductance for sodium and potassium, indicating that glutamic acid-95 is a crucial constituent of the ion selectivity filter. There were only minor differences in the crystal structures of mutant and wild-type annexin V around the mutation site; however, the mutant showed structural differences elsewhere, including the presence of a calcium binding site in domain III unrelated to the mutation. Analysis of the membrane-bound form of annexin V by electron microscopy revealed no differences between the wild type and mutant.

In eukaryotic cells, the vast majority of proteins in the cytosol and nucleus are degraded via the proteasome-ubiquitin pathway. The 26S proteasome is a huge protein degradation machine of 2.5 MDa, built of approximately 35 different subunits. It contains a proteolytic core complex, the 20S proteasome and one or two 19S regulatory complexes which associate with the termini of the barrel-shaped 20S core. The 19S regulatory complex serves to recognize ubiquitylated target proteins and is implicated to have a role in their unfolding and translocation into the interior of the 20S complex where they are degraded into oligopeptides. While much progress has been made in recent years in elucidating the structure, assembly and enzymatic mechanism of the 20S complex, our knowledge of the functional organization of the 19S regulator is rather limited. Most of its subunits have been identified, but specific functions can be assigned to only a few of them.

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A model for the calculation of the scalar, position-dependent static dielectric function of an ensemble consisting of polarizable sites and of free relaxing point dipoles at fixed positions is proposed. It is based on classical electrostatics and leads to an iteration equation or nonlinear partial differential equation for the local dielectric constant. The expressions contain the equations of Debye, Onsager, and Neumann as special cases and thus might be considered as an extension to inhomogeneous matter. The model may have applications in the case of biological macromolecules in particular proteins where the polar side chains can be identified with the model’s dipoles. The algorithm leads to a position dependent dielectric constant in the protein interior in contrast to the assumption of a homogeneous permittivity throughout the protein. By taking into account the dielectric fine structure inside the macromolecules we hope that our approach may help to improve continuum electrostatic models of these molecules. The relevant polarizabilities and dipole moments of the amino acids are given and their corresponding local dielectric constants are estimated as a first approximation based on the Onsager and Kirkwood equations.