Structural and Functional Modeling of Artificial Bioactive Proteins

A total of 32 synthetic proteins designed by Michael Hecht and co-workers was investigated using standard bioinformatics tools for the structure and function modeling. The dataset consisted of 15 artificial α-proteins (Hecht_α) designed to fold into 102-residue four-helix bundles and 17 artificial six-stranded β-sheet proteins (Hecht_β). We compared the experimentally-determined properties of the sequences investigated with the results of computational methods for protein structure and bioactivity prediction. The conclusion reached is that the dataset of Michael Hecht and co-workers could be successfully used both to test current methods and to develop new ones for the characterization of artificially-designed molecules based on the specific binary patterns of amino acid polarity. The comparative investigations of the bioinformatics methods on the datasets of both de novo proteins and natural ones may lead to: (1) improvement of the existing tools for protein structure and function analysis; (2) new algorithms for the construction of de novo protein subsets; and (3) additional information on the complex natural sequence space and its relation to the individual subspaces of de novo sequences. Additional investigations on different and varied datasets are needed to confirm the general applicability of this concept.