The bait-CBD fusion and the plain CBD are bound to separate cellulose columns and stringently washed to remove all proteins except bait or CBD. The columns are incubated with lysate from Hbt.salinarum cells grown in synthetic medium containing 12C-leucine (bait) or Selleckchem APO866 13C-leucine (pMS4), respectively. After elution, the eluates are pooled. To discriminate specific interaction partners from nonspecific binders, we combined the purification procedure
with stable isotope labeling by amino acids in cell culture (SILAC) [58, 59]. For this, a second Hbt.salinarum strain which expresses the bait protein under the same strong promoter as in the bait-CBD strain but without CBD fusion, the bait-control strain, was used. Both strains were treated equally with the exception that the bait-CBD strain was grown in medium containing 13C6-leucine while the bait-control strain was grown in medium containing 12C6-leucine. Lysates from both strains were pooled and affinity
purification was done from the pooled lysate. Finally, the ratio between the relative amount of the 12C-form and the 13C-form of the identified proteins (the SILAC ratio) was determined. To allow easier visualization, a symmetrical measure, called association DAPT chemical structure score, was calculated from the SILAC ratio as described in the methods section. The association score indicates if an identified protein was specifically enriched by binding to the respective bait: in case of a specific interactor mainly the 13C-form would be present in the eluate, whereas for unspecific binders the 13C- and the 12C-form would be present to nearly the same extent. Proteins with an association score greater BCKDHA than seven were considered to be interactors and all other proteins to be nonspecific binders (for details see Additional file 2). In our second method, two-step bait fishing (Figure 1B), lysates from the bait-CBD strain
and a CBD-control strain (which expresses the plain CBD under the same promoter used for the bait-CBD fusions) were applied to separate cellulose columns. A stringent washing step followed which removed (nearly) all bound proteins except the bait-CBD fusion protein or the CBD, respectively. The bait-CBD loaded cellulose column was then incubated with lysate from Hbt.salinarum wildtype cells grown with 12C6-leucine, while the CBD-loaded column was incubated with lysate from Hbt.salinarum wildtype cells grown with 13C6-leucine. After careful washing to remove unbound proteins, the EX 527 purchase bait-prey complexes which formed on column were eluted, the eluates pooled, and proteins identified by mass spectrometry. Determination of the association score to discriminate specific and unspecific binders was done as for one-step bait fishing. In two-step bait fishing, the SILAC labeling was reversed compared to one-step bait fishing.