Synthesis, purification and initial structural characterization of octarellin, a de novo polypeptide modelled on the α/β-barrel Proteins

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Abstract
We have attempted to construct an artificial polypeptide that folds like the eight-stranded parallel β-barrel structures. Our approach consists of repeating eight times a unit peptide designed to adopt a ‘β-strand/α-helix’ pattern. A first ‘test’ sequence for this structural unit was deduced from a series of parameters defined after an analysis of three natural α/β-barrel proteins and including principally the lengths of the secondary structure elements, the α/β packing and the fitting on average Garnier profiles. The gene encoding this structural unit was synthesized, cloned and expressed in Escherichia coli either as a monomer or as direct repeats of 2–12 units. Preliminary structural characterization of the 7-, 8- and 9-fold unit polypeptides by circular dichroism measurements indicates the presence of the predicted amount of α-helix in the three proteins. Further analysis by urea-gradient gel electrophoresis demonstrates that, in the conditions tested, only the 8-fold unit polypeptide forms a compact structure through a cooperative and rapid two-state folding transition involving long-range molecular interactions.