1
|
van Tol BDM, van Doodewaerd BR, Lageveen-Kammeijer GSM, Jansen BC, Talavera Ormeño CMP, Hekking PJM, Sapmaz A, Kim RQ, Moutsiopoulou A, Komander D, Wuhrer M, van der Heden van Noort GJ, Ovaa H, Geurink PP. Neutron-encoded diubiquitins to profile linkage selectivity of deubiquitinating enzymes. Nat Commun 2023; 14:1661. [PMID: 36966155 PMCID: PMC10039891 DOI: 10.1038/s41467-023-37363-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 03/13/2023] [Indexed: 03/27/2023] Open
Abstract
Deubiquitinating enzymes are key regulators in the ubiquitin system and an emerging class of drug targets. These proteases disassemble polyubiquitin chains and many deubiquitinases show selectivity for specific polyubiquitin linkages. However, most biochemical insights originate from studies of single diubiquitin linkages in isolation, whereas in cells all linkages coexist. To better mimick this diubiquitin substrate competition, we develop a multiplexed mass spectrometry-based deubiquitinase assay that can probe all ubiquitin linkage types simultaneously to quantify deubiquitinase activity in the presence of all potential diubiquitin substrates. For this, all eight native diubiquitins are generated and each linkage type is designed with a distinct molecular weight by incorporating neutron-encoded amino acids. Overall, 22 deubiquitinases are profiled, providing a three-dimensional overview of deubiquitinase linkage selectivity over time and enzyme concentration.
Collapse
Affiliation(s)
- Bianca D M van Tol
- Department of Cell and Chemical Biology, Chemical Biology and Drug Discovery, Leiden University Medical Center, 2333 ZC, Leiden, The Netherlands
| | - Bjorn R van Doodewaerd
- Department of Cell and Chemical Biology, Chemical Biology and Drug Discovery, Leiden University Medical Center, 2333 ZC, Leiden, The Netherlands
| | | | - Bas C Jansen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333 ZA, Leiden, The Netherlands
| | - Cami M P Talavera Ormeño
- Department of Cell and Chemical Biology, Chemical Biology and Drug Discovery, Leiden University Medical Center, 2333 ZC, Leiden, The Netherlands
| | - Paul J M Hekking
- Department of Cell and Chemical Biology, Chemical Biology and Drug Discovery, Leiden University Medical Center, 2333 ZC, Leiden, The Netherlands
| | - Aysegul Sapmaz
- Department of Cell and Chemical Biology, Chemical Biology and Drug Discovery, Leiden University Medical Center, 2333 ZC, Leiden, The Netherlands
| | - Robbert Q Kim
- Department of Cell and Chemical Biology, Chemical Biology and Drug Discovery, Leiden University Medical Center, 2333 ZC, Leiden, The Netherlands
| | - Angeliki Moutsiopoulou
- Department of Cell and Chemical Biology, Chemical Biology and Drug Discovery, Leiden University Medical Center, 2333 ZC, Leiden, The Netherlands
| | - David Komander
- Ubiquitin Signalling Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Melbourne, Victoria, Australia
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333 ZA, Leiden, The Netherlands
| | - Gerbrand J van der Heden van Noort
- Department of Cell and Chemical Biology, Chemical Biology and Drug Discovery, Leiden University Medical Center, 2333 ZC, Leiden, The Netherlands
| | - Huib Ovaa
- Department of Cell and Chemical Biology, Chemical Biology and Drug Discovery, Leiden University Medical Center, 2333 ZC, Leiden, The Netherlands
| | - Paul P Geurink
- Department of Cell and Chemical Biology, Chemical Biology and Drug Discovery, Leiden University Medical Center, 2333 ZC, Leiden, The Netherlands.
| |
Collapse
|
2
|
Abstract
In this issue of Cell Chemical Biology,De Cesare et al. (2018) report the development of a high-throughput assay that measures E2/E3 enzyme activity by MALDI-TOF mass spectrometry and apply this to screen for small molecule E3 inhibitors. This assay potentially accelerates the drug discovery for the ubiquitin ligation pathway.
Collapse
Affiliation(s)
- Bianca D M van Tol
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Paul P Geurink
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Huib Ovaa
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands.
| |
Collapse
|
3
|
Xin BT, van Tol BDM, Ovaa H, Geurink PP. Native chemical ligation at methionine bioisostere norleucine allows for N-terminal chemical protein ligation. Org Biomol Chem 2018; 16:6306-6315. [DOI: 10.1039/c8ob01627e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
γ-Thionorleucine is synthesized and used for N-terminal chemical protein modification by native chemical ligation–desulfurization to prepare linear diubiquitin.
Collapse
Affiliation(s)
- Bo-Tao Xin
- Oncode Institute and Department of Cell and Chemical Biology
- Leiden University Medical Center
- 2333 ZC Leiden
- The Netherlands
| | - Bianca D. M. van Tol
- Oncode Institute and Department of Cell and Chemical Biology
- Leiden University Medical Center
- 2333 ZC Leiden
- The Netherlands
| | - Huib Ovaa
- Oncode Institute and Department of Cell and Chemical Biology
- Leiden University Medical Center
- 2333 ZC Leiden
- The Netherlands
| | - Paul P. Geurink
- Oncode Institute and Department of Cell and Chemical Biology
- Leiden University Medical Center
- 2333 ZC Leiden
- The Netherlands
| |
Collapse
|
4
|
Geurink PP, van Tol BDM, van Dalen D, Brundel PJG, Mevissen TET, Pruneda JN, Elliott PR, van Tilburg GBA, Komander D, Ovaa H. Development of Diubiquitin-Based FRET Probes To Quantify Ubiquitin Linkage Specificity of Deubiquitinating Enzymes. Chembiochem 2016; 17:816-20. [PMID: 26996281 PMCID: PMC4922411 DOI: 10.1002/cbic.201600017] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Indexed: 11/20/2022]
Abstract
Deubiquitinating enzymes (DUBs) are proteases that fulfill crucial roles in the ubiquitin (Ub) system, by deconjugation of Ub from its targets and disassembly of polyUb chains. The specificity of a DUB towards one of the polyUb chain linkages largely determines the ultimate signaling function. We present a novel set of diubiquitin FRET probes, comprising all seven isopeptide linkages, for the absolute quantification of chain cleavage specificity of DUBs by means of Michaelis–Menten kinetics. Each probe is equipped with a FRET pair consisting of Rhodamine110 and tetramethylrhodamine to allow the fully synthetic preparation of the probes by SPPS and NCL. Our synthetic strategy includes the introduction of N,N′‐Boc‐protected 5‐carboxyrhodamine as a convenient building block in peptide chemistry. We demonstrate the value of our probes by quantifying the linkage specificities of a panel of nine DUBs in a high‐throughput manner.
Collapse
Affiliation(s)
- Paul P Geurink
- Department of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands.
| | - Bianca D M van Tol
- Department of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
| | - Duco van Dalen
- Department of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
| | - Paul J G Brundel
- Department of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
| | - Tycho E T Mevissen
- Medical Research Council Laboratory of Molecular Biology, FrancisCrick Avenue, Cambridge, CB2 0QH, UK
| | - Jonathan N Pruneda
- Medical Research Council Laboratory of Molecular Biology, FrancisCrick Avenue, Cambridge, CB2 0QH, UK
| | - Paul R Elliott
- Medical Research Council Laboratory of Molecular Biology, FrancisCrick Avenue, Cambridge, CB2 0QH, UK
| | - Gabriëlle B A van Tilburg
- Department of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
| | - David Komander
- Medical Research Council Laboratory of Molecular Biology, FrancisCrick Avenue, Cambridge, CB2 0QH, UK
| | - Huib Ovaa
- Department of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands.
| |
Collapse
|