A strategy for modulation of enzymes in the ubiquitin system.
Andreas Ernst,George V. Avvakumov,Jiefei Tong,Yihui Fan,Yanling Zhao,Philipp Alberts,Avinash Persaud,John R. Walker,Ana-Mirela Neculai,Dante Neculai,Andrew Vorobyov,Pankaj Garg,Linda G. Beatty,Pak-Kei Chan,Yu Chi Juang,Marie-Claude Landry,Christina Yeh,Christina Yeh,Elton Zeqiraj,Konstantina Karamboulas,Abdellah Allali-Hassani,Masoud Vedadi,Mike Tyers,Mike Tyers,Jason Moffat,Frank Sicheri,Frank Sicheri,Laurence Pelletier,Laurence Pelletier,Daniel Durocher,Daniel Durocher,Brian Raught,Daniela Rotin,Jianhua Yang,Michael Moran,Sirano Dhe-Paganon,Sirano Dhe-Paganon,Sachdev S. Sidhu +37 more
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TLDR
This work used massively diverse combinatorial libraries of ubiquitin variants to develop inhibitors of four deubiquitinases (DUBs) and analyzed the DUB-inhibitor complexes with crystallography to report a method to target the myriad enzymes that govern ubiquitination of protein substrates.Abstract:
The ubiquitin system regulates virtually all aspects of cellular function. We report a method to target the myriad enzymes that govern ubiquitination of protein substrates. We used massively diverse combinatorial libraries of ubiquitin variants to develop inhibitors of four deubiquitinases (DUBs) and analyzed the DUB-inhibitor complexes with crystallography. We extended the selection strategy to the ubiquitin conjugating (E2) and ubiquitin ligase (E3) enzymes and found that ubiquitin variants can also enhance enzyme activity. Last, we showed that ubiquitin variants can bind selectively to ubiquitin-binding domains. Ubiquitin variants exhibit selective function in cells and thus enable orthogonal modulation of specific enzymatic steps in the ubiquitin system.read more
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Patent
Method and systems for investigating the ubiquitin-proteasome system
Manfred Auer,Joanna Koszela +1 more
TL;DR: In this article, a method for investigating molecular interactions and enzyme activities related to the ubiquitin-proteasome system (UPS) is provided, the method comprising: providing at least one surface with a target moiety bound to at least a portion thereof, exposing said surface to a medium comprising a labelled ubiquitins, SUMO, NEDD8 e.t.c.
Posted ContentDOI
Flexibility and design: conformational heterogeneity along the evolutionary trajectory of a redesigned ubiquitin
TL;DR: In this article, the authors exploited advances in multiconformer modeling of room temperature X-ray data collection on redesigned ubiquitin variants selected for increasing binding affinity to the deubiquitinase USP7.
Journal ArticleDOI
Generation of ubiquitin-based binder with an inserted active peptide.
TL;DR: The ubiquitin-based binder (UbB), into which the p53 (17-28) peptide was inserted between Ile36 and Pro37, indicated that UbB maintained a similar structure to that of ubiquitIn, which indicates that ubiquit in is a robust scaffold for peptide grafting.
Structural and functional studies of the papain-like protease 2 from mouse hepatitis virus
TL;DR: This work aims to establish a system to investigate how the DUB and deISGylating activities of CoV PLPs are involved in virus immune evasion and chose PLP2 from mouse hepatitis to do so.
Posted ContentDOI
Climbing up and down binding landscapes: a high-throughput study of mutational effects in homologous protein-protein complexes
Michael Heyne,Michael Heyne,Jason Shirian,Itay Cohen,Yoav Peleg,Evette S. Radisky,Niv Papo,Julia M. Shifman +7 more
TL;DR: This study studies the effect of tens of thousands of single and double mutations on binding affinity of three homologous protease-inhibitor complexes and shows that binding landscapes of the three complexes are strikingly different and depend on the PPI evolutionary optimality.
References
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Book
Molecular Cloning: A Laboratory Manual
TL;DR: Molecular Cloning has served as the foundation of technical expertise in labs worldwide for 30 years as mentioned in this paper and has been so popular, or so influential, that no other manual has been more widely used and influential.
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Airlie J. McCoy,Ralf W. Grosse-Kunstleve,Paul D. Adams,Martyn Winn,Laurent C. Storoni,Randy J. Read +5 more
TL;DR: A description is given of Phaser-2.1: software for phasing macromolecular crystal structures by molecular replacement and single-wavelength anomalous dispersion phasing.
Journal ArticleDOI
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TL;DR: The likelihood function for macromolecular structures is extended to include prior phase information and experimental standard uncertainties and the results derived are consistently better than those obtained from least-squares refinement.