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Computational protein design has progressed rapidly over the last years. A number of design methods have been proposed and tested. In this paper, we report the successful application of a fragment-based method for protein design. The method uses statistical information on tetrapeptide backbone conformations. The previously published artificial fold of TOP 7 (Kuhlman et al., Science, 2003; 302:1364-1368) was chosen as template. A series of polypeptide sequences were created that were predicted to fold into this target structure. Two of the designed proteins, M5 and M7, were expressed and characterized by fluorescence spectroscopy, circular dichroism and NMR. They showed the hallmarks of well-ordered tertiary structure as well as cooperative folding/unfolding transitions. Furthermore, the two novel proteins were found to be highly stable against temperature and denaturant-induced unfolding., (2007 Wiley-Liss, Inc.)

We studied a number of physicochemical parameters of transfection-active peptide-DNA complexes including size, aggregation behaviour and circular dichroism (CD) spectra. These data were brought in relationship to the transfection activity of these peptides in order to better understand the mechanism of peptide-mediated gene transfer. A DNA binding oligolysine (K(16)) and a peptide comprising K(16) with an added peptide loop containing the arbitrary sequence RAD not known as a receptor ligand were used. Whereas the K(16)-DNA complex at 88% charge neutralization of the DNA phosphates collapsed into small toroidal particles with a diameter of 200 nm by dynamic light scattering, K(16)-cRAD did not. Instead, large aggregates were observed. CD spectra showed that the K(16)-DNA complexes were in a -psi state observed at liquid crystalline phases. Increasing positive charge by addition of further K(16) or disturbing the -psi state by introducing the RAD-peptide loop resulted in increasing instability indicated by aggregation and loss of the -psi CD spectrum of the complexes. Transfection experiments indicated that the aggregated material was the transfection-active component.

Relationships between the structure of transfecting complexes of histone H1 and DNA and their transfection efficiency were studied. Transfection activity proved to be connected to complex aggregates. Low speed centrifugation of the complexes resulted in loss of the transfection activity. The complexes/aggregates were active with high efficiency in a broad range of weight input ratios r(i) (0.1 < r(i) < 30). Using atomic force microscopy (AFM), the complexes were imaged at negative, nearly electroneutral and positive charge conditions. Electroneutral complexes at r(i) = 1 showed a multitude of different complex forms. Fibrillar, network-like and branched structures were frequently present in one complex. Strongly positive charged complexes had a toroidal appearance. All these different forms contributed to the high transfection efficiency. Cellular uptake is supposed to be by phagocytosis.

Using polycationic transfection one encounters undesired persistent binding to cells of sticky polycation/DNA complexes. These complexes simulate transfection under conditions where no uptake is expected e.g. at 4 degrees C if the uptake is by endocytosis. To overcome this problem, using H1/DNA complexes, we developed an easy and nontoxic method for removing the sticky complexes not taken up during the transfection phase. The cells are simply washed with isotonic (0.1 M) MgCl2 solution, which enables the complete removal of the complexes by their rapid dissolution.

We introduced galactose and a short RGD sequence as ligands into H1 histone to target the asialoglycoprotein receptor or integrins on cells expressing these receptors. The efficiency of the gene transfer mediated by galactosylated H1 histone was strongly affected by the transfection conditions. Galactosylation of H1 led to an increase of the basic H1-mediated gene transfer activity only, when H1 itself did not develop its optimal transfection activity. Under other conditions any specific gene transfer mediated by the asialoglycoprotein receptor was covered by the high transfection efficiency of H1 itself. Similar results of a marginal increase in the transfection efficiency were obtained by conjugates of a short RGD sequence and H1. This unexpected failure in the receptor specificity of both conjugates could be due to the unspecific cell-binding capacity of the H1 moiety and to increasing solubility of the complexes as shown by gel shift and solubility measurements.