HDX-MS of TRAPPII reveals a conserved Rab binding interface

We used hydrogen deuterium exchange mass spectrometry (HDX-MS) to define the interface of TRAPPII with three Rab GTPases (Rab1, Rab11, Rab43). These experiments were performed in the presence of EDTA to generate a nucleotide free stabilised Rab-GEF complex. Significant decreases in deuterium incorporation (defined as >4%, >0.4Da, two tailed T-test p value <0.01) were identified in the TRAPPC2L, TRAPPC4, and TRAPPC5 in the presence of Rab GTPases with no other changes in other TRAPP subunits. Here we show that all three Rab GTPases bind at a conserved interface of TRAPPII.