Project coworkers and collaborators
We study the creation of new proteins and protein variants. The purpose of this work is to use such engineered proteins to enable research and applications which have been very difficult or even impossible so far. Examples of our endeavors are the creation of new engineered binding proteins for applications in biotechnology, to inhibit other proteins or to kill tumor cells in therapy, or the stabilization of proteins so that they can be studied structurally and biophysically, such as G-protein-coupled receptors evolved to high stability and expression levels for drug screening and structural studies.
One of our main areas of interest have been novel scaffolds for selective binding (e.g. the DARPin technology we have developed), or other repeat proteins such as the Armadillo Repeat Proteins. Because of the complexity of these tasks, this research requires a highly interdisciplinary approach, combining detailed biophysical studies, computer modeling and advanced molecular biology, especially directed evolution. In most projects also structure determination is needed by crystallography carried out in the research group, or in collaboration, by NMR or cryo electron tomography.
Some projects also bridge protein engineering with applications, in cell biology or, in the case of tumor targeting testing in animal models.
Role of UZH within the PRe-ART Consortium
The main role of UZH within this project will be directed evolution experiments, structure determination and evaluation of binding and sequence discrimination.
Hansen, S., Ernst, P., König, S. L. B., Reichen, C., Ewald, C., Nettels, D., Mittl, P. R. E., Schuler, B. and Plückthun, A. (2018). Curvature of designed armadillo repeat proteins allows modular peptide binding. J. Struct. Biol. 201, 108-117.
Hansen, S., Kiefer, J. D., Madhurantakam, C., Mittl, P. R. E. and Plückthun, A. (2017). Structures of designed armadillo repeat proteins binding to peptides fused to globular domains. Protein Sci. 26, 1942-1952.
Ernst, P. and Plückthun, A. (2017). Advances in the design and engineering of peptide-binding repeat proteins. Biol. Chem. 398, 23-29.
Reichen, C., Hansen, S., Forzani, C., Honegger, A., Fleishman, S. J., Zhou, T., Parmeggiani, F., Ernst, P., Madhurantakam, C., Ewald, C., Mittl, P. R., Zerbe, O., Baker, D., Caflisch, A. and Plückthun, A. (2016). Computationally designed armadillo repeat proteins for modular peptide recognition. J. Mol. Biol. 428, 4467-4489.
Hansen, S., Tremmel, D., Madhurantakam, C., Reichen, C., Mittl, P. R. and Plückthun, A. (2016). Structure and energetic contributions of a designed modular peptide-binding protein with picomolar affinity. J. Am. Chem. Soc. 138, 3526-3532.
Reichen, C., Madhurantakam, C., Hansen, S., Grütter, M. G., Plückthun, A. and Mittl, P. R. (2016). Structures of designed armadillo-repeat proteins show propagation of inter-repeat interface effects. Acta Crystallogr. D Struct. Biol. 72, 168-175.
Ewald, C., Christen, M. T., Watson, R. P., Mihajlovic, M., Zhou, T., Honegger, A., Plückthun, A., Caflisch, A. and Zerbe, O. (2015). A combined NMR and computational approach to investigate peptide binding to a designed Armadillo repeat protein. J. Mol. Biol. 427, 1916-1933.
Reichen, C., Madhurantakam, C., Plückthun, A. and Mittl, P. R. (2014). Crystal structures of designed armadillo repeat proteins: implications of construct design and crystallization conditions on overall structure. Protein Sci. 23, 1572-1583.
Watson, R. P., Christen, M. T., Ewald, C., Bumbak, F., Reichen, C., Mihajlovic, M., Schmidt, E., Guntert, P., Caflisch, A., Plückthun, A. and Zerbe, O. (2014). Spontaneous self-assembly of engineered armadillo repeat protein fragments into a folded structure. Structure 22, 985-995.
Reichen, C., Hansen, S. and Plückthun, A. (2014). Modular peptide binding: From a comparison of natural binders to designed armadillo repeat proteins. J. Struct. Biol. 185, 147-162.
Varadamsetty, G., Tremmel, D., Hansen, S., Parmeggiani, F. and Plückthun, A. (2012). Designed Armadillo repeat proteins: library generation, characterization and selection of peptide binders with high specificity. J. Mol. Biol. 424, 68-87.
Alfarano, P., Varadamsetty, G., Ewald, C., Parmeggiani, F., Pellarin, R., Zerbe, O., Plückthun, A. and Caflisch, A. (2012). Optimization of designed armadillo repeat proteins by molecular dynamics simulations and NMR spectroscopy. Protein Sci. 21, 1298-1314.
Madhurantakam, C., Varadamsetty, G., Grütter, M. G., Plückthun, A. and Mittl, P. R. (2012). Structure-based optimization of designed Armadillo-repeat proteins. Protein Sci. 21, 1015-1028.
Parmeggiani, F., Pellarin, R., Larsen, A. P., Varadamsetty, G., Stumpp, M. T., Zerbe, O., Caflisch, A. and Plückthun, A. (2008). Designed armadillo repeat proteins as general peptide-binding scaffolds: consensus design and computational optimization of the hydrophobic core. J. Mol. Biol. 376, 1282-1304.