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Computational Modeling of Designed Ankyrin Repeat Protein Complexes with Their Targets.

  • Radom F Department of Biochemistry, University of Zurich, Zurich, Switzerland.
  • Paci E Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.
  • Plückthun A Department of Biochemistry, University of Zurich, Zurich, Switzerland. Electronic address: plueckthun@bioc.uzh.ch.
  • 2019-05-15
Published in:
  • Journal of molecular biology. - 2019
ClusPro
DARPin
Rosetta
homology modeling
protein–protein docking
Animals
Ankyrin Repeat
Crystallography, X-Ray
Databases, Protein
Humans
Molecular Docking Simulation
Protein Binding
Protein Conformation
Proteins
English Recombinant therapeutic proteins are playing an ever-increasing role in the clinic. High-affinity binding candidates can be produced in a high-throughput manner through the process of selection and evolution from large libraries, but the structures of the complexes with target protein can only be determined for a small number of them in a costly, low-throughput manner, typically by x-ray crystallography. Reliable modeling of complexes would greatly help to understand their mode of action and improve them by further engineering, for example, by designing bi-paratopic binders. Designed ankyrin repeat proteins (DARPins) are one such class of antibody mimetics that have proven useful in the clinic, in diagnostics and research. Here we have developed a standardized procedure to model DARPin-target complexes that can be used to predict the structures of unknown complexes. It requires only the sequence of a DARPin and a structure of the unbound target. The procedure includes homology modeling of the DARPin, modeling of the flexible parts of a target, rigid body docking to ensembles of the target and docking with a partially flexible backbone. For a set of diverse DARPin-target complexes tested it generated a single model of the complex that well approximates the native state of the complex. We provide a protocol that can be used in a semi-automated way and with tools that are freely available. The presented concepts should help to accelerate the development of novel bio-therapeutics for scaffolds with similar properties.
Language
  • English
Open access status
green
Identifiers
Persistent URL
https://sonar.ch/global/documents/128585
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