2017 Fiscal Year Annual Research Report
Chemical Biology Studies of Ubiquitin Transfer with Synthetic Proteins
| Project/Area Number |
17H01211
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| Research Institution | Nagoya University |
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Principal Investigator |
Bode Jeffrey 名古屋大学, トランスフォーマティブ生命分子研究所, 客員教授 (90727900)
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| Co-Investigator(Kenkyū-buntansha) |
望田 啓子 (桑田啓子) 名古屋大学, トランスフォーマティブ生命分子研究所, 特任助教 (70624352)
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| Project Period (FY) |
2017-04-01 – 2022-03-31
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| Keywords | タンパク質化学 / ケミカルバイオロジー / 有機合成化学 / ユビキチン / プロテオーム解析 |
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| Outline of Annual Research Achievements |
In this project we chemically synthesise ubiquitin E2 ligases as probes. We have recently completed a new chemical synthesis of Ubiquitin by a two segment strategy. This approach allows us to flexibly introduce photo affinity labels and modulate the sites of further ubiquitination. These molecules serve as platform for the development of molecular probes for ubiquitination pathways. We have also just recently identified a synthetic route to the E2 ligase UbcH5a by a three fragment, 2-ligation strategy. By using two-KAHA ligations with 5-oxaproline we can conversantly prepare the protein containing two homoserine residues. In parallel, we are developing new monomers that lead to natural residues at the ligation site. Based on our experience with the synthesis of Ubc9, the SUMO E2 ligase, we will fold UbcH5A and characterize its ubiquitination activity in a biochemical assay. We have also made progress on establishing a proteomics workflow for analysing covalent conjugates of ubiquitin E2 ligases with modifier proteins. These methods will be adapted to our specific probes and proteins of interest.
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| Current Status of Research Progress |
Current Status of Research Progress
1: Research has progressed more than it was originally planned.
Reason
With the first synthesis of UbcH5A complete, we are currently in process of scaling up the segment synthesis and planning for the preparation of analogues containing unnatural amino acids. We intended to utilise our synthetic E2 enzymes to trap the unknown ubiquitin E3 ligases involved in ubiquitination of proteins. To achieve this, we are currently preparing a number of unnatural amino acids containing photo affinity tags. The synthesis of these special amino acids takes some time but is progressing well. By incorporating these into various sites of the synthetic protein, we will be able to trap E3 ligases responsible for promoting the ubiquitination of target proteins. We are currently conducting biochemical characterisation of the synthetic E2 enzymes, particularly with regard to their ability to conjugate ubiquitin or other modifier proteins.
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| Strategy for Future Research Activity |
The identification of unknown E3 ligases is currently in high demand among biologist. We are working with biological groups at ITbM to identify specific proteins of interest that are known to be ubiquitinated. In most cases, we do not know which E2 or E3 ligase is involved. To identify the unknown E2 ligase, we are preparing special variants of Ubq that will allow us to find out which E2 is responsible for the conjugation. As UbcH5A is one of the most common E2 ligases, we hope to identify a couple of proteins of interest that operate with this enzyme and design synthetic probes to trap the unknown E3 ligases. As there are more than 1000 E3 enzymes, this can be challenging but we believe our unique combination of synthetic proteins and proteomic capabilities will allow us to establish a platform for rapid identification of the enzymes involved in ubiquitin transfer. The same principles can be applied to other E2 enzymes or even to other classes of modifier proteins.
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