ClustalW alignment In order to perform the alignment, amino acid sequences from different vertebrate species annotated as Bax isoform alpha [human (Q07812), rat (Q63690), mouse (Q07813), bovine (O022703)] or complete sequences having an equivalent start codon assignment [cat (Q8SQ43), dog (Q8HYUS), zebra fish (Q919N4)] as well as having only a short extension [xenopus (Q98U13)] were used. Sequences with N-terminal extensions or deletions within the sequence were excluded, e.g. the sequence from Pan troglodytes (chimpanzee), which shows only two differences in the part homologous to the human Bax alpha, but is elongated by 70 amino acids at the N-terminus.
Expression and purification of human Bax alpha We essentially followed the procedure described by Suzuki et al. (2000) (link). The purity of the protein was analyzed by SDS-PAGE and LC-MS (calculated mass: 21,184 Da; determined mass: 21,183 Da).
Bax reconstitution in liposomes Lipid mixtures from E. coli or bovine heart extracts (Avanti polar lipids Inc. Alabaster, AL) were dissolved in chloroform, dried by evaporation to form a thin film, and resuspended in buffer 1 (20 mM Tris-HCl, 100 mM NaCl; pH 7.5) by repeatedly vortexing, freezing and thawing. The final lipid concentration was 20 mg/ml. The solution was passed through a membrane with 200 or 400 nm pores (Avestin Inc. Ottawa, Canada) for at least 25 times. Bax pre-incubated with 0.1% DDM was mixed with the vesicles pre-incubated with 0.1% DDM to a final concentration of 0.25 mg/ml protein and 12 mg/ml lipid. Biobeads (BioRAD, Hercules, CA) were added to remove excess detergent. For protein insertion the solution was incubated for 3 h at 30 °C at 300 rpm. To remove free protein as well as aggregates, a nycodenz gradient was used. The gradient was layered as followed: the liposome/Bax solution in 10% nycodenz (dissolved in buffer 1) was overlaid with 5% nycodenz in buffer 1 and finally pure buffer 1. The gradient was spun at 200,000×g for 30 min at 10 °C. A pellet and a swimming lipid band (fuzzy when bovine heart lipids were used) were separated. The latter was mixed with buffer 1 and centrifuged under identical conditions to remove the nycodenz by sedimentation.
Secondary structure determination by circular-dichroism spectroscopy The concentration of Bax (in buffer 2; 20 mM Tris, pH 8.8) was adjusted to 0.1 mg/ml. The CD-spectra and melting curves were recorded on a Jasco J715 spectropolarimeter (Jasco, Gross Umstadt, Germany) with a Jasco PFD 350S Peltier type FDCD attachment for temperature control using a 0.1 mm quartz cuvette. Two spectra were accumulated per measurement using a data pitch of 0.1 nm, a scan speed of 20 nm s−1 and 1 nm slit width. The content of secondary structure was calculated using the program CDNN (Bohm et al. 1992 (link)). Notably, samples of Bax did not show any precipitation during the temperature increase which was tested by UV-spectroscopy. If buffer 1 was used instead of buffer 2, only neglectable differences were visible in the spectra.
Protease digestion Monomeric and oligomeric Bax samples were mixed with subtilisin or proteinase K at a stoichiometry of 1:200 and incubated for one hour on ice. The reaction was stopped either by (a) treatment with the denaturing SDS-gel loading buffer and subsequent boiling for 5 min or (b) freezing in liquid nitrogen and storage at −80 °C before further analysis. Protein samples were subjected to SDS-PAGE and blotted onto a PVDF membrane (transfer buffer: 25 mM Tris-HCl, 192 mM glycine, 20% methanol) for subsequent N-terminal sequencing of individual bands (using a gas-phase sequencer Procise 492cLC, Applied Biosystems, Foster City, CA). Sample mixtures were also analyzed by ESI-MS. After Bax reconstitution in liposomes, the protein concentration was estimated by the band intensity on a SDS-gel. Consequently, the estimation was less accurate than the estimation by UV spectroscopy. Furthermore, since ESI-MS did not work with Bax liposomes only N-terminal sequencing was performed.
Tryptophan fluorescence Fluorescence emission spectra were recorded on a Perkin-Elmer spectrometer (LS50B, Waltham MA). Bax (concentrations of 0.25 to 1 µM), and free acetylated-tryptophan (4 µM) were excited at 280 nm at a slit width of 5 nm to detect the emitted fluorescence in the range between 300 and 400 nm.
Cross-link experiments Protein samples were adjusted to a concentration of about 0.5 mg/ml in the presence or absence of 0.5% DDM. These samples were slowly heated to 50–90 °C and the temperature was kept constant for 600 s. Afterwards, the samples were immediately cooled on ice. 10 µl samples were mixed with 1 µl ammonium peroxydisulfate (APS, 25 mM) and 2 µl ruthenium (II) Tris-bipyridyldication (5 mM Sigma-Aldrich) in the dark and then immediately exposed to illumination with visible light (400 to 700 nm, generated by a Xenon lamp, 100 W Leica, filters: KG4, GG 395 nm). The photo-induced reaction was stopped by the addition of 5 µl SDS-gel loading buffer.
Miscellaneous To induce oligomerization, Bax was mixed with 0.5% DM (Anatrace), 0.5% DDM (Anatrace) or 2% OG (Anatrace) in buffer 1. The samples were incubated under shaking for at least 8 h at 4 °C. The oligomerization was analyzed by size exclusion chromatography on a Superdex 200 column using SMART FPLC (GE Healthcare). ESI-MS was performed on a micrOTOF LC (Bruker Daltonics, Billerica, MA). Absorption spectra were collected on a Shimadzu UV-1700 UV-visible spectrophotometer. Bax structure was illustrated with Pymol using the PDB file 1F16 of monomeric Bax (Suzuki et al. 2000 (link)). Data were plotted using origin 6.1.