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Guided example 3 – building a protein structural model
Scenario
Jan is interested in interleukin 1-receptor-associated kinases (IRAKs) as possible targets for cancer therapy. Several mutations in IRAK2 are associated with cancers, so Jan would like to investigate IRAK2 as a possible new target. There are quite a few small-molecule inhibitors available for related proteins and Jan wants to know whether they’d be likely to bind to IRAK2. However, there is no crystal structure available for the kinase domain of IRAK2, so Jan wants to model the structure to see whether it’s likely to resemble the 3D structures of other IRAKs.
Over the next two pages, you will be guided through two different ways to model IRAK2 structure. The first (on the following page) consists of retrieving the predicted IRAK2 structure from AlphaFold DB. The second is using homology modelling – the process of estimating a theoretical structure of a protein by building a structural template from homologous sequences and threading your sequence to this template and optimising it.