DC10: Structural studies of transport and binding

There are no accurate models for how trimeric autotransporters (TAAs) bind host effectors; all of the studies so far have involved mutagenesis and foot-printing. We aim to rectify this gap. AlphaFold does a poor job of modelling these structures and complexes (1) because they have unusual sequences and (2) because they aren't globular.

The project involves studying TAAs from ESKAPE pathogens (eg. Acinetobacter) to determine how they bind host effectors (collagen, laminin etc) via cryoEM and structural EPR spectroscopy (with Christos Pliotas, University of Manchester). The student will then connect this information to strain and variant differences/changes in virulence, as this will lead to improvements in diagnostics. We will then extend this work to model how invasins, related proteins, from at least one ESKAPE pathogen studied in StraDiVarious (K. pneumoniae and E. cloacae) bind their targets. Finally, we will model how the inside-out barrels insert into the membrane by studying the (BAM-invasin complex), building on work by our collaborator (Dirk Linke, University of Oslo). The project will allow both academic and industry secondments, using state of the art structural biology equipment.

Methods will include protein expression and purification of membrane proteins, as well as EPR spectroscopy (in Manchester) and cryoEM, both locally and on secondment. Modelling the complex with the latest tools and the validation of those models through mutagenesis will also be a key part of the techniques used.