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Predicting the Substrate Specificity of Proteases
Dr. James Whisstock, Department of Biochemistry and Molecular Biology, Faculty of Medicine.
The main of this project is to investigate whether the structure of a protease in complex with a substrate improves researchers' abilities to predict substrate specificity. Structural comparison of different protease / substrate / inhibitor complexes reveal that the backbone conformation of the substrate P3-P3’ residues interact with the active site of a protease in a predictable or canonical fashion. Thus, it may be possible to predict the preference each subsite has for a particular amino acid. Accordingly, the project aims to investigate whether automated modelling of a substrate can be used to glean useful information in regards to substrate specificity.
The key objectives of the project are:
- To build a pipeline for generation of useful protease/substrate models,
- To develop approaches to rank these protease/substrate models using structural data alone,
- To compare these predictions with published experimentally-derived data.
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