2022 Fiscal Year Research-status Report
Regulation of NF-kB signaling through competitive interactions against linear polyubiquitin
| Project/Area Number |
22K06161
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| Research Institution | Kyoto University |
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Principal Investigator |
Walinda Erik 京都大学, 医学研究科, 助教 (80782391)
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| Project Period (FY) |
2022-04-01 – 2025-03-31
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| Keywords | ubiquitin / ubiquitin binding / M1-linked chains / HOIL-1L / NZF domain / zinc finger |
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| Outline of Annual Research Achievements |
The study has progressed smoothly and produced a range of outcomes that have been disseminated through publication. Notably, the research on ubiquitin chains using molecular dynamics simulations and NMR experiments has yielded intriguing findings that support observations made by researchers in other fields, such as X-ray crystallography. Specifically, researchers have reported diverse conformations of the same ubiquitin chain under different crystallization conditions, but all of these conformations have been found to be situated along the same phase-space trajectory as identified by molecular dynamics. As a result, we are making progress in understanding the relationship between the internal dynamics of ubiquitin chains and their subsequent binding and release from ubiquitin-binding receptors. However, we are still investigating the precise kinetics of the HOIL-1L NZF-linear ubiquitin interaction and starting to comprehend how competitive processes may contribute to polyubiquitin binding selectivity and avidity. The primary outcome of the first year has been submitted for publication. However, future aspects of the study, particularly those involving chain binders other than the HOIL-1L NZF domain, are still unpublished and will be analyzed starting this year.
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| Current Status of Research Progress |
Current Status of Research Progress
2: Research has progressed on the whole more than it was originally planned.
Reason
The research progress was moderately smooth due to competing projects conducted in parallel, particularly international collaborations that required significant analysis time. While the obtained results were intriguing and satisfactory, the involvement in other projects created some hindrances in the research timeline and productivity. Further measures could be taken to ensure better allocation of research resources and optimize the utilization of available time to maximize the research outcome.
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| Strategy for Future Research Activity |
The research plan for academic year 2023 involves an analysis of the kinetics of HOIL-1L binding to polyubiquitin at the atomic scale, focusing on the contribution of the individual amino acids using NMR spectroscopy and mathematical modelling. Competitive binding assays will be conducted using A20, NEMO, and other linear polyubiquitin binding proteins. The study aims to assess the relative change in binding kinetics under these conditions, providing insights into the competitive nature of polyubiquitin binding selectivity and avidity.
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| Causes of Carryover |
Participation at international conference in Boston, US was cancelled, thus changing the total cost for this year.
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