A Structure-Based Strategy for Engineering Selective Ubiquitin Variant Inhibitors of Skp1-Cul1-F-Box Ubiquitin Ligases

Structure
Maryna GorelikFrank Sicheri

Abstract

Skp1-Cul1-F-box (SCF) E3 ligases constitute the largest and best-characterized family of the multisubunit E3 ligases with important cellular functions and numerous disease links. The specificity of an SCF E3 ligase is established by one of the 69 human F-box proteins that are recruited to Cul1 through the Skp1 adaptor. We previously reported generation of ubiquitin variants (UbVs) targeting Fbw7 and Fbw11, which inhibit ligase activity by binding at the F-box-Skp1 interface to competitively displace Cul1. In the present study, we employed an optimized engineering strategy to generate specific binding UbVs against 17 additional Skp1-F-box complexes. We validated our design strategy and uncovered the structural basis of binding specificity by crystallographic analyses of representative UbVs bound to Skp1-Fbl10 and Skp1-Fbl11. Our study highlights the power of combining phage display with structure-based design to develop UbVs targeting specific protein surfaces.

References

Apr 5, 1987·Journal of Molecular Biology·S Vijay-KumarW J Cook
Jun 6, 2000·Trends in Biochemical Sciences·Y WangS H Bryant
Apr 19, 2002·Nature·Ning ZhengNikola P Pavletich
Jun 3, 2004·Genome Research·Gavin E CrooksSteven E Brenner
Jul 21, 2004·Journal of Computational Chemistry·Eric F PettersenThomas E Ferrin
Dec 2, 2004·Acta Crystallographica. Section D, Biological Crystallography·Paul Emsley, Kevin Cowtan
Oct 7, 2005·Genome Biology·Peter J StogiosGilbert G Privé
Mar 23, 2006·Acta Crystallographica. Section D, Biological Crystallography·Jay Painter, Ethan A Merritt
Aug 8, 2007·Journal of Molecular Biology·Evgeny Krissinel, Kim Henrick
Aug 1, 2007·Journal of Applied Crystallography·Airlie J McCoyRandy J Read
Feb 4, 2010·Acta Crystallographica. Section D, Biological Crystallography·Wolfgang Kabsch
Feb 4, 2010·Acta Crystallographica. Section D, Biological Crystallography·Paul D AdamsPeter H Zwart
Jun 29, 2010·Nature Biotechnology·Stephen OrlickyMike Tyers
Nov 28, 2012·Nature Chemical Biology·Yingnan ZhangJacob E Corn
Dec 25, 2012·Chemistry & Biology·Lily WuTimothy J Cardozo
Jan 5, 2013·Science·Andreas ErnstSachdev S Sidhu
Jan 30, 2014·The Journal of Biological Chemistry·Susan LoreyUlrich Haupts
Nov 15, 2014·Nature Reviews. Drug Discovery·Jeffrey R SkaarMichele Pagano
Mar 16, 2016·Proceedings of the National Academy of Sciences of the United States of America·Maryna GorelikSachdev S Sidhu
Jan 1, 1997·Methods in Enzymology·Zbyszek Otwinowski, Wladek Minor
Nov 7, 2017·Cell·Justin M ReitsmaRaymond J Deshaies

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Citations

Sep 1, 2020·The FEBS Journal·Nicole LeBlancWei Zhang
Feb 29, 2020·Pharmacological Reviews·Bo ZhaoJun Yin
Jul 28, 2019·Proceedings of the National Academy of Sciences of the United States of America·Edmond R WatsonBrenda A Schulman
Apr 19, 2020·Current Opinion in Structural Biology·Martin L RennieHelen Walden
Jun 13, 2021·Protein Engineering, Design & Selection : PEDS·Chen T LiangWei Zhang

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