5MFK

Designed armadillo repeat protein YIII(Dq.V1)4CPAF in complex with peptide (KR)4

Summary for 5MFK

• Entry DOI: 10.2210/pdb5mfk/pdb
• Descriptor: YIII(Dq.V1)4CPAF, (KR)4 (3 entities in total)
• Functional Keywords: designed armadillo repeat protein, peptide binding, de novo protein
• Biological source: synthetic construct; More
• Total number of polymer chains: 4
• Total formula weight: 54029.10

Authors

Hansen, S.,Ernst, P.,Reichen, C.,Ewald, C.,Mittl, P.,Plueckthun, A. (deposition date: 2016-11-18, release date: 2017-09-13, Last modification date: 2024-05-08)

Primary citation

Hansen, S.,Ernst, P.,Konig, S.L.B.,Reichen, C.,Ewald, C.,Nettels, D.,Mittl, P.R.E.,Schuler, B.,Pluckthun, A.
Curvature of designed armadillo repeat proteins allows modular peptide binding.
J. Struct. Biol., 201:108-117, 2018

PubMed Abstract: Designed armadillo repeat proteins (dArmRPs) were developed to create a modular peptide binding technology where each of the structural repeats binds two residues of the target peptide. An essential prerequisite for such a technology is a dArmRP geometry that matches the peptide bond length. To this end, we determined a large set (n=27) of dArmRP X-ray structures, of which 12 were previously unpublished, to calculate curvature parameters that define their geometry. Our analysis shows that consensus dArmRPs exhibit curvatures close to the optimal range for modular peptide recognition. Binding of peptide ligands can induce a curvature within the desired range, as confirmed by single-molecule FRET experiments in solution. On the other hand, computationally designed ArmRPs, where side chains have been chosen with the intention to optimally fit into a geometrically optimized backbone, turned out to be more divergent in reality, and thus not suitable for continuous peptide binding. Furthermore, we show that the formation of a crystal lattice can induce small but significant deviations from the curvature adopted in solution, which can interfere with the evaluation of repeat protein scaffolds when high accuracy is required. This study corroborates the suitability of consensus dArmRPs as a scaffold for the development of modular peptide binders.

PubMed: 28864298
DOI: 10.1016/j.jsb.2017.08.009

Experimental method

X-RAY DIFFRACTION (2.3 Å)