No abstract

The Arc repressor, which is involved in the switch between lysis and lysogeny of Salmonella bacteriophage P22, does not belong to any of the known classes of DNA-binding proteins. Mutagenesis studies show that the DNA-binding region is located in the 15 N-terminal amino-acid residues. We have now determined the three-dimensional structure of the Arc dimer from an extensive set of interproton-distance data obtained from 1H NMR spectroscopy. A priori, intra- and inter-monomer nuclear Overhauser effects (NOEs) cannot be distinguished for a symmetric dimer. But by using the homology with the Escherichia coli Met repressor we could interpret the NOEs unambiguously in an iterative structure refinement procedure. The final structure satisfies a large set of NOE constraints (1,352 for the dimer). It shows a strongly intertwined dimer, in which residues 8-14 of different monomers form an antiparallel beta-sheet. A model for the Arc repressor-operator complex can account for all available biochemical and genetic data. In this model two Arc dimers bind with their beta-sheet regions in successive major grooves on one side of the DNA helix, similar to the Met repressor interaction. Thus, Arc and Met repressors are members of the same family of proteins, which contain an antiparallel beta-sheet as the DNA-binding motif.

Rennet-induced casein gels made from skim milk were studied rheologically. A scaling model or framework for describing the rheological behavior of gels is discussed and used for classification of the structure of casein gels. There are two main parameters in the model that describe the number of deformable links in a strand and the bendability of the links. In the model at least five types of gel structure can be distinguished. Application of the model to experimental data on rennet-induced casein gels at pH of 6.0–6.6 and 25 °C shows that they contain straight strands with a large number of deformable links. Analysis of the experimental data of the storage modulus, maximum linear strain and yield stress as a function of the volume fraction results in the same information about the gel structure.

A study is presented on the structure of rennet(-induced) casein or skim milk gels at three pH values (5.3, 6.0, and 6.65) and temperatures (20, 25, and 30°C). The structure was examined by confocal scanning laser microscopy and permeametry. Deconvolution was applied to the microscopic images. A fractal scaling analysis has been applied to the images and permeametry results. In this analysis, the fractal dimensionality (Df), lower cutoff length (R0), and apparent pore size (P) of the linear scaling regime were calculated from the microscopical data. The Df and apparent pore size were also calculated from the permeametry data. During aging of the gels, a coarsening of the structure was observed; the pore size increased and the clusters became more compact. This was reflected in the fractal parameters: R0 and P increased during gel aging. Their values are generally high (0.5-1.5 and 5.0-15 µm, respectively) compared to data obtained by computer simulations. The Df value is also high (∼2.2-2.6), which is an indication of slow aggregation or rearrangements during aggregation. The gel aging effects are probably mainly due to rearrangements such as particle fusion and strand fracture, which rates increase with increasing temperature, and even more pronouncedly, with decreasing pH.

In this paper we simulate the aggregation of interacting particles using Brownian dynamics. The parameters varied are volume fraction and interaction potential well depth. At volume fractions above 0.07 percolated structures are observed; these are formed differently from cluster-cluster aggregation. Fractal analysis of the structures shows nonuniversal fractal scaling for all systems, with lower bound r 0 and fractal dimensionality d f . Both of these properties depend on the simulation parameters and on time. Compactification in time leads to an increasing r 0 and a decreasing d f , that is, structures with thick strands. This effect is most pronounced at large well depths. Due to compactification in time, percolated states can be transient.