COMISIONES DE EVALUACIÓN Y DE PROMOCION

3.2.4.1 Determination of protein concentration

Total protein concentration of cell lysates was determinated spectrophotometrically at OD595 using Bradford reagent (Pierce) (Bradford, 1976) and compared to a BSA standard

dilution series. The concentration of the samples was then normalized.

3.2.4.2 SDS polyacrylamide gel electrophoresis (SDS-PAGE)

Proteins were analyzed by SDS-PAGE using a discontinuous buffer system under denaturing and reducing conditions (Laemmli, 1970). 4x concentrated SDS loading buffer was added to protein samples prior to denaturation at 95 °C for 5 min and gel loading. Gels (0.75 or 1 mm width) had varying polyacrylamide concentrations (7.5 – 15 %) depending on the required resolution. Electrophoresis was performed in BioRad Mini-Protean II employing a constant voltage of 200 V in SDS running buffer.

Stacking Gel 5.1 % acrylamide/bisacrylamide (37.5:1), 125 mM Tris HCl, pH 6.8, 0.1 % SDS, 0.1 % TEMED, 0.1 % APS

Separating Gel 7.5 - 15 % acrylamide/bisacrylamide (37.5:1), 750 mM Tris HCl, pH 8.8, 0.1 % SDS, 0.075 % TEMED, 0.05 % APS 4x SDS loading buffer 62.5 mM Tris-HCl, pH 6.8, 20 % glycerol, 2 % SDS, 0,005 %

bromphenol blue, 750 mM 2-mercaptoethanol

SDS running buffer 50 mM Tris-Base (pH8.3), 380 mM glycine, 0.1 % SDS

3.2.4.3 Western Blotting

Proteins, separated by SDS-PAGE, were transferred onto nitrocellulose membranes (Protran, Schleicher&Schuell) in a semi-dry blotting unit (SemiPhore). The electrophoretic protein transfers were achieved in Western blot buffer at a constant current of approximately 0.5 – 0.8 mA/cm2 gel size for 1 h (Towbin et al., 1979). Transfer efficiency was verified by brief incubation of nitrocellulose membranes into PonceauS solution. Membranes were blocked in PBS-T supplemented either with 3 % BSA or with 4 % skim milk powder for 1 h at RT or at over night at 4 °C. Subsequently membranes were incubated with the primary antibody diluted 1:200-1:10000 in PBS-T supplemented with either 0.3 % BSA or 0.4 % skim milk powder for 1 h at RT. After extensively washing in PBST, membranes were incubated with a 1:1000-1:10000 dilution of secondary antibody conjugated to horseradish peroxidase as above described. Finally, membranes were washed as before. Protein bands were detected

Material and Methods 52 by incubating membranes with ECL solutions A and B at 1:1 ratio and exposing to either X- ray films (Amersham) or luminescent image analyzer LAS3000 (Fujifilm).

Western blot buffer 50 mM Tris (pH 8.4), 192 mM glycine, 20 % methanol PonceauS solution 2.5 % PonceauS, 40 % methanol, 5 % acetic acid

PBS-T PBS, 0.05 % TWEEN-20

ECL-A 1 ml 250 mM 3-aminophthalhydrazid (Luminol), 444 µl 90 mM p-coumarin acid, 10 ml 1 M Tris-HCl, pH 8.5, ddH20 to

100 ml final volume.

ECL-B 61.4 µl 30 % ddH20, 10 ml 1 M Tris-HCl, pH 8.5, ddH20

to 100 ml final volume.

3.2.4.4 Dot blot assay

Dot blot assay was also used to detect proteins but in contrast to Western blot, protein samples were neither denatured nor separated electrophoretically. Typically, 5 µl protein samples (total cell extracts or gel filtration fractions) were spotted directly onto nitrocellulose membrane. The membrane was then air-dried and processed as described above.

3.2.4.5 In vitro HttExon1-Aggregation

Purified GST-Htt20Q and GST-Htt53Q (Muchowski et al., 2000) were obtained from the laboratory stock of the Department of Cellular Biochemistry, Max-Planck Institute of Biochemistry, Martinsried, Germany. Aggregation of GST-Htt proteins (3µM) was initiated by addition of 2.5 U PreScission protease (Amersham) in aggregation buffer at 30oC for 5 h. For recruitment analysis, 45 µl of gel filtration fraction were added.

Aggregation buffer 50 mM Tris-HCl, pH 7.5, 150 mM KCl, 1 mM DTT, 0.1 mg/ml Ovalbumin, 1x protease inhibitor mix

3.2.4.6 Filter retardation assay

To detect SDS-insoluble aggregates, cell extracts or in vitro aggregation reactions were mixed with an equal volume of 4% SDS and 100 mM DTT and heated (95°C, 5 min), followed by filtration through a cellulose acetate membrane (0.2 µm pore size) and immunodetection (Scherzinger et al., 1997; Muchowski et al., 2000).

Material and Methods 53

3.2.4.7 Size exclusion chromatography

Total cell extracts were centrifuged at either 20.000 x g or 100.000 x g for 30 min or 1 h and subjected to size exclusion chromatography on FPLC or SMART system with Superdex200 or Superose6 column at 4 °C or 15 °C, respectively. The appropriate lysis buffer was used as running buffer. Fractions were analyzed by immunoblotting and quantification software AIDA. The chromatographic resolution was between 2000 and 17 kDa determined by protein standards.

3.2.4.8 Immunoprecipitation

Cell lysates were blocked with 50 µl protein A sepharose and BSA at a final concentration of 1 % for 1 h at 4 °C in order to prevent unspecific binding. After removal of protein A sepharose by centrifugation at 2000 x g, cell lysates were transferred to mini- columns and incubated with 1 – 2 µg primary antibodies over night at 4 °C with agitation. Subsequently 50 µl protein A sepharose were added to the antigen-antibody complex and incubated for 1 – 2 h at 4 °C. Protein A sepharose was washed extensively with cell lysis buffer TG&P. Finally, the bound antibody and antigen complex was incubated in SDS loading buffer at 95 °C for 5 min and eluted by centrifugation.

3.2.4.9 Ni-NTA pull down of His-tagged proteins

Cell lysates were incubated with Ni-NTA resin pre-equilibrated in lysis buffer TP (Qiagen; 50 µl of 1:1 slurry) in micro spin columns (MoBiTec, Germany) over night at 4 °C. Beads were washed three times with lysis buffer TP. Bound proteins were eluted from the resin with lysis buffer TP (supplemented with 400 mM Imidazole pH 7.5). Samples were removed during washing for analysis. Equal amount of eluate and control samples were mixed with 4x SDS loading buffer and incubated at 95 °C for 5 min.

3.2.4.10 Trichloracetic acid (TCA)-precipitation

TCA precipitation was performed to concentrate protein samples prior to SDS-PAGE analysis. Protein samples were mixed at 1:1 ratio with a 20 % TCA solution and incubated for 30 min on ice. After centrifugation at 20.000 x g for 20 min at 4 °C, pellets were washed with 500 µl of acetone (-20 °C) and pelleted again. Proteins were then resuspended in SDS loading buffer.

Results 54