Exploring the repeat protein universe through computational protein design

Fabio Parmeggiani
BBSRC/EPSRC Synthetic Biology Research Centre, University of Bristol, UK
Friday, november 25 2016, 2pm, Salle 2/124 (see map)

Structural biology has shown the broad range of structures produced by polypeptide chains. The variety we observe today was shaped by evolutionary pressure, but it is unclear how likely it is for proteins to form structures not yet observed in Nature. To investigate this question, we used novel computationally designed proteins formed by modular repeating units and we explored the range of achievable geometries. Repeats were formed by two helices of variable length designed with the Rosetta macromolecular modeling suite. Out of 83 proteins selected for experimental characterization, 54% possessed the expected secondary structure and were monomeric and stable up to 95°C and 3M guanidine hydrochloride. The designs were validated by small angle X-ray scattering and 15 crystal structures confirmed the accuracy of the designs. The results indicate that it is possible to explore a large part of the protein universe not found in Nature. Moreover, the ability to efficiently design repeat proteins opens the way to the development of novel customized biological tools for applications in nanotechnology and medicine.

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