Protein expression and purification
Rab proteins were expressed and purified as described previously (Rab1 [Schoebel et al., 2009] and other Rab proteins [Bleimling et al., 2009]) and preparatively loaded with GppNHp (Guanosine-5’-[β-γ-Imido]-triphosphat) for interaction studies with their effector proteins. For this purpose, the proteins were incubated in the presence of 5 mM EDTA, 5–10% glycerol, three-fold molar excess of GppNHp over the Rab protein and 0.5 units alkaline phosphatase per mg Rab protein for 2 hr at 20°C or at 4°C overnight. Subsequently the proteins were purified via gel filtration in a buffer containing 20 mM Hepes pH 7.5, 50 mM NaCl, 2 mM DTE, 2 mM MgCl2 and 10 µM GppNHp. bMERB domains (amino acid boundaries and Uniprot accession IDs are shown in Figure 6—figure supplement 3) were cloned into a modified pET19 expression vector and proteins were expressed in E. coli BL21 DE3 RIL cells (growth at 37°C to OD600 nm = 0.8–1.0, stored at 4°C for 30 min, expression was induced by addition of 0.3–0.5 mM IPTG and cells were grown for 14–18 hr at 20°C). Subsequently the proteins were purified by Ni2+-affinity chromatography, cleavage of the His6-tag with TEV-protease and a second Ni2+-affinity purification. Final purification was achieved by gel filtration (Rabs: 20 mM Hepes pH 7.5, 50 mM NaCl, 2 mM DTE, 2 mM MgCl2, 10 µM GDP or GppNHp; Micals: 20 mM Hepes pH 7.5, 50 or 100 mM NaCl, 2 mM DTE). In order to express the selenomethionine labeled version of the coiled coil domain of Mical-3, the methionine biosynthesis inhibition method (Van Duyne et al., 1993) was used. The labeled protein was purified as described above. FTase and GGTase I were purified as described previously (Dursina et al., 2006; Kalinin et al., 2001).
For prenylation, EHBP11047-1231/EHBP1L11340-1523, substrate (farnesyl pyrophosphate (FPP) or geranylgeranyl pyrophosphate (GGPP); Sigma) and prenyltransferase (FTase or GGTase I) were mixed in a 1:5:0.5 ratio in buffer containing 25 mM Hepes pH 7.2, 40 mM NaCl and 2 mM MgCl2 and incubated for 3 hr at room temperature. To check the extent of prenylation, samples were analyzed by ESI-MS.