Radom, F, Paci, E orcid.org/0000-0002-4891-2768 and Plückthun, A (2019) Computational Modeling of Designed Ankyrin Repeat Protein Complexes with their Targets. Journal of Molecular Biology, 431 (15). pp. 2852-2868. ISSN 0022-2836
Abstract
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.
Metadata
Item Type: | Article |
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Authors/Creators: |
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Copyright, Publisher and Additional Information: | Crown Copyright © 2019 Published by Elsevier Ltd. This is an author produced version of a paper published in the Journal of Molecular Biology. Uploaded in accordance with the publisher's self-archiving policy. |
Keywords: | DARPin; Protein–protein docking; Homology modeling; Rosetta; ClusPro |
Dates: |
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Institution: | The University of Leeds |
Academic Units: | The University of Leeds > Faculty of Biological Sciences (Leeds) > School of Molecular and Cellular Biology (Leeds) |
Depositing User: | Symplectic Publications |
Date Deposited: | 15 May 2019 13:45 |
Last Modified: | 11 May 2020 00:39 |
Status: | Published |
Publisher: | Elsevier Inc. |
Identification Number: | 10.1016/j.jmb.2019.05.005 |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:146071 |
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