VAPB/ALS8 interacts with FFAT-like proteins including the p97 cofactor FAF1 and the ASNA1 ATPase

Table 2 TRC complex subunits slightly accumulate in endogenous VAPB immunoprecipitates upon proteasome inhibition

Protein name	UniProt ID	MW (Da)	SILAC ratio L/H^a
Protein name	UniProt ID	MW (Da)	L + MG 2 hr	H + MG 2 hr	L + MG 6 hr	H + MG 6 hr
ASNA1	O43681	38,793	1.31 ± 0.08 (31)	0.79 ± 0.07 (27)	1.42 ± 0.10 (32)	0.87 ± 0.06 (35)
BAG6	P46379	119,409	1.47 ± 0.18 (36)	0.77 ± 0.11 (36)	1.43 ± 0.19 (52)	0.94 ± 0.10 (43)
GET4	Q7L5D6	36,504	1.39 ± 0.11 (8)	0.73 ± 0.06 (11)	1.30 ± 0.08 (9)	0.84 ± 0.03 (13)
UBL4A	P11441	17,777	1.50 ± 0.10 (7)	0.74 ± 0.04 (9)	1.51 ± 0.15 (7)	0.89 ± 0.04 (10)

^aLight- (L) and heavy-labeled (H) cells were treated with MG132 (MG) for 2 or 6 hr, as indicated. Equal amounts of light- and heavy-labeled extracts were mixed and endogenous VAPB was immunoprecipitated using specific antibodies. The light/heavy SILAC ratios (L/H) determined by mass spectrometry are indicated. L + MG indicates that the light-labeled samples were treated with MG132. Proteins whose interaction with VAPB is stimulated by proteasome inhibition accumulate in these samples, resulting in L/H ratios higher than 1. H + MG indicates that the heavy-labeled samples were treated with MG132. Protein accumulation in the heavy-labeled samples results in L/H ratios lower than 1. The L/H for proteins that are not affected by proteasome inhibition will be close to 1. The numbers in parenthesis represent the number of spectra analyzed for each sample.

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