(BBSRC DTP) Catalytic landscapes of floppy enzymes: modelling with distance constraints from non-native amino acid probes

Enzymes are Nature’s machines – they catalyse the myriad reactions that make life possible and can be exploited as biocatalysts for the synthesis of a range of useful products. In order to understand how enzymes work, which is both essential to understand their role in health and to effectively engineer them as new biocatalysts, we must understand what they look like. Atomic-resolution structures of protein and enzymes are routinely solved using X-ray crystallography, but this method tends to fail when the protein has dynamic or disordered regions – i.e. when the protein is floppy. One approach to investigate the structure of floppy proteins is to solve the structure of individual structured domains, then use molecular modelling and molecular dynamics simulations to build models of the full-length protein. This approach is greatly enhanced if experimental distance constraints can be built into the modelling. Further, if these distance constraints can be continually measured during e.g. enzyme turnover, then it is possible to use them to create molecular movies that show how the enzyme moves during catalysis.

Förster resonance energy transfer (FRET) and pulsed EPR (e.g. DEER) experiments can be used to measure distances between two fluorophores or spin labels, respectively, in proteins. In some case cases, intrinsic fluorophores (tryptophan or some cofactors) or radicals (semiquinones, some metal centres) can be used for such measurements. If not, extrinsic fluorescent probes and spin labels are used by covalent attachment, typically to surface-exposed cysteine residues on the protein. This gets messy when two different fluorescent probes are needed for FRET experiments and/or when the protein has many existing surface cysteines. This project will move beyond this state-of-the art to use a range of non-native amino acids as both fluorescence probes and spin labels to study the structure and dynamics of a range of biocatalytically useful enzymes. ‘Clickable’ non-native amino acids will also be used to label cysteine-rich enzymes. These labelled enzymes will be studied by both fluorescence and EPR techniques, with the resulting distances fed into molecular dynamics simulations to build structures and movies of floppy enzymes in order to understand how they work, and how to (re)engineer them for future roles in biocatalysis.

www.manchester.ac.uk/research/sam.hay/
https://sites.google.com/site/scruttonlab/

Contact for further Information
For more details contact Dr S Hay ([Email Address Removed])