Design of bioinspired tandem ubiquitin binding domains as tools to investigate the ubiquitin-modified proteome
Lead Research Organisation:
University of Nottingham
Department Name: School of Life Sciences
Abstract
Deciphering the ubiquitin code
Post-translational modification of proteins with ubiquitin regulates a myriad of biological processes. Versatility arises from ubiquitin's ability to form structurally unique polyubiquitin chains, varying according to linkage (isopeptide and peptide), which become attached to selected lysine residues of a target protein. Recent studies show that this 'ubiquitin code' is expanded by additional post-translation modifications including acetylation and phosphorylation.
Non-covalent recognition of polyubiquitin chains by specific effector proteins (ubiquitin-binding proteins) underlies the respective biological process that is regulated. Recognition of (poly)ubiquitin is mediated by ubiquitin-binding domains (UBDs), found within these ubiquitin-binding proteins, which recognise distinct surface patches on ubiquitin. However despite the vast complexity of ubiquitin modifications and the array of biological processes that are known to be controlled by ubiquitin, only a handful of ubiquitin-binding proteins have been functionally verified and characterised to date. Further, the full range UBDs capable of discriminating phosphorylated ubiquitin from unmodified ubiquitin remain to be identified.
We hypothesise that there are many unconventional UBDs, including with specificity for phosphorylated ubiquitin, that have been completely overlooked due to the limitations of current purification methods and informatics approaches.
In this project we are using a combination of novel biochemical, phage display and sequence analysis approaches to search for and identify these 'missing links' (ubiquitin-binding proteins and UBDs) which must exist in order to connect ubiquitin modifications to known biological outputs. Emphasis is placed on UBDs that recognise additional post-translational modifications such as phosphorylation. For selected proteins, the mechanistic basis for their abilities to act as effectors will be probed by characterising their interactions with ubiquitin using state-of-the-art structural biology and biophysical approaches, in order to place observations on a firm molecular and quantitative footing.
Post-translational modification of proteins with ubiquitin regulates a myriad of biological processes. Versatility arises from ubiquitin's ability to form structurally unique polyubiquitin chains, varying according to linkage (isopeptide and peptide), which become attached to selected lysine residues of a target protein. Recent studies show that this 'ubiquitin code' is expanded by additional post-translation modifications including acetylation and phosphorylation.
Non-covalent recognition of polyubiquitin chains by specific effector proteins (ubiquitin-binding proteins) underlies the respective biological process that is regulated. Recognition of (poly)ubiquitin is mediated by ubiquitin-binding domains (UBDs), found within these ubiquitin-binding proteins, which recognise distinct surface patches on ubiquitin. However despite the vast complexity of ubiquitin modifications and the array of biological processes that are known to be controlled by ubiquitin, only a handful of ubiquitin-binding proteins have been functionally verified and characterised to date. Further, the full range UBDs capable of discriminating phosphorylated ubiquitin from unmodified ubiquitin remain to be identified.
We hypothesise that there are many unconventional UBDs, including with specificity for phosphorylated ubiquitin, that have been completely overlooked due to the limitations of current purification methods and informatics approaches.
In this project we are using a combination of novel biochemical, phage display and sequence analysis approaches to search for and identify these 'missing links' (ubiquitin-binding proteins and UBDs) which must exist in order to connect ubiquitin modifications to known biological outputs. Emphasis is placed on UBDs that recognise additional post-translational modifications such as phosphorylation. For selected proteins, the mechanistic basis for their abilities to act as effectors will be probed by characterising their interactions with ubiquitin using state-of-the-art structural biology and biophysical approaches, in order to place observations on a firm molecular and quantitative footing.
Organisations
Studentship Projects
| Project Reference | Relationship | Related To | Start | End | Student Name |
|---|---|---|---|---|---|
| BB/M008770/1 | 01/10/2015 | 31/10/2024 | |||
| 1647712 | Studentship | BB/M008770/1 | 01/10/2015 | 30/09/2019 |
| Description | Ubiquitin is a post-translational modification of proteins, and allows the diversification of highly-specific cell and biochemical signalling events, involved in practically every cell biological process. The ubiquitin signal is decoded by ubiquitin-binding domains (UBD) within ubiquitin-binding proteins (UBP), but there is an obvious lack of knowledge on the known population of UBDs and UBPs. This project has identified a novel UBP and a potential novel UBD, moving forward our knowledge of ubiquitin's control of biochemical events. |
| Exploitation Route | Further characterisation of the UBP is required, especially with regards to its biological function. The pathways related to ubiquitin-recognition by this novel UBP are currently unknown, so further study would reveal extra layers of biochemical control and provide context for the interaction. Indeed, there are very few known functions of this UBP in its own right, so any studies would go a long way towards establishing a biological function of this little-understood protein. |
| Sectors | Other |
| Description | Development of engagement resources |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Other audiences |
| Results and Impact | Created engagement resources for activities at undergrad recruitment events, patient days and regional community engagement days. Resources aimed at enabling other University researchers to apply their work to public-interest topics with plenty of hand-on activities. Topics combined history, archaeology, medicine and biochemical research to access new audiences previously un-engaged with one or more of the topics. |
| Year(s) Of Engagement Activity | 2020 |