Design of de novo enzymes to catalyse novel reactions

The aim of the project is to design de novo proteins to help improve our understanding of natural proteins, particularly allosteric sensors and enzymes, and to introduce function into de novo protein scaffolds. The Woolfson lab specialises in the design of alpha-helical coiled-coil peptides and proteins, a structure formed when helices wrap around each other. While nature primarily uses dimers to tetramers, the lab has designed larger oligomers, including barrels with open cavities. My project will use these scaffolds and introduce function.
A major challenge in de novo protein design is introducing dynamics. Designed proteins, including the lab's coiled coils, tend to be highly stable and likely more rigid structures than those found in nature. Natural enzymes are dynamic; they change shape when binding substrates or in response to environment.

In this project I will explore various ways to design dynamic de novo proteins. For example, by attaching multiple domains together, and "frustrating" the most stable conformations of each domain. We will then attempt to stabilise one conformer over another, for example by having charge interactions that only occur under certain pH conditions, with a readout being investigated by NMR spectroscopy.

By introducing such switches, the de novo proteins could be used as components a biological sensor. Natural enzymes often catalyse reactions either between multiple substrates, or with the assistance of cofactors, which are bound either covalently or non-covalently to the protein. Previous work in the lab has introduced such binding and catalysis to hyper-stable structures, and my aim is to introduce this to the dynamic scaffolds as they are designed.

The design and characterisation of these new protein scaffolds fits within the 'synthetic biology' and 'chemical biology and biological chemistry' research areas, whilst enzyme design fits within 'catalysis.