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Titles and Legends to Supplementary Tables and Figures Supplementary Table S1. CML patient sample details. WBC (G/l): white blood count (grams/liter); Hb (g/dl): hemoglobin (grams/deciliter); Plt (G/l): platelets (grams/liter); Basos: basophils; pb: peripheral blood; CRP (mg/dl): c-reactive protein (milligrams/deciliter); HU (mg/d): hydroxyurea (mg/day); n.t. not tested. Supplementary Table S2a. All proteins purified on the INNO-406 matrix from K562 lysate. Proteins are sorted by the number of identified unique peptides (Peptide Count) in pulldown 1 (PD1). Proteins listed have at least one specific peptide that confirms the presence of the protein in the pulldown. IPI_IDs are IPI protein database entries to which identified peptides were assigned. PD1 and PD2 refer to the duplicate pulldowns performed for each cell type. Competitive refers to pulldowns where lysates were pre-treated with 20 µM INNO-406 before incubation with the matrix. Core proteome refers to the most abundant proteins in the K562 total cell lysate, which were also present in the INNO-406 pulldowns. Frequent Hitters refers to proteins identified from the corresponding cell type on matrices of five kinase-inhibitor-unrelated drugs (paroxetine, amphotericin B, ciprofloxacin, daunorubicin and kanamycin). Potential targets are subtracted from right to left based on 1) lack of presence in duplicate experiments, 2) presence in the Frequent Hitter experiments, 3) presence in the Core Proteome and 4) lack of competition. Protein kinases are indicated by bold print. The remaining, and therefore most confident INNO-406 targets, are marked in red. Supplementary Table S2b. All proteins purified on the INNO-406 matrix from KU812 lysate. Proteins are sorted by the number of identified unique peptides (Peptide Count) in pulldown 1 (PD1). Proteins listed have at least one specific peptide that confirms the presence of the protein in the pulldown. IPI_IDs are IPI protein database entries to which identified peptides were assigned. PD1 and PD2 refer to the duplicate pulldowns performed for each cell type. Competitive refers to pulldowns where lysates were pre-treated with 20 µM INNO-406 before incubation with the matrix. Frequent Hitters refers to proteins identified from the corresponding cell type on matrices of five kinase-inhibitorunrelated drugs (paroxetine, amphotericin B, ciprofloxacin, daunorubicin and kanamycin). Potential targets are subtracted from right to left based on 1) lack of presence in duplicate experiments, 2) 1 presence in the Frequent Hitter experiments and 3) lack of competition. Protein kinases are indicated by bold print. The remaining, and therefore most confident INNO-406 targets, are marked in red. Supplementary Table S2c. All proteins purified on the INNO-406 matrix from CML chronic phase patient pool lysate. Proteins are sorted by the number of identified unique peptides (Peptide Count) in pulldown 1 (PD1). Proteins listed have at least one specific peptide that confirms the presence of the protein in the pulldown. IPI_IDs are IPI protein database entries to which identified peptides were assigned. PD1 and PD2 refer to the duplicate pulldowns performed for each cell type. Competitive refers to pulldowns where lysates were pre-treated with 20 µM INNO-406 before incubation with the matrix. Frequent Hitters refers to proteins identified from the corresponding cell type on a matrix of the kinase-inhibitor-unrelated drug paroxetine. Potential targets are subtracted from right to left based on 1) lack of presence in duplicate experiments, 2) presence in the Frequent Hitter experiment and 3) lack of competition. Protein kinases are indicated by bold print. The remaining, and therefore most confident INNO-406 targets, are marked in red. Supplementary Table S3. List of frequent hitters identified in K562 or KU812 total cell lysates. Five structurally kinase inhibitor-unrelated drugs (paroxetine, amphotericin B, ciprofloxacin, daunorubicin and kanamycin) were directly immobilized via their amino groups on Sepharose beads as previously described (Rix, 2007). The resulting matrices were exposed either to K562 (Table S3a) or KU812 (Table S3b) total cell lysates. All proteins identified in each experiment are shown in the list. Proteins are sorted by the number of times identified across the five drugs. The higher the incidence amongst the experiments, the more likely the protein is to be a non-specific "frequent hitter" and selecting it as a "real" target of the drug of interest should be done with caution. IPI-IDs are IPI protein database entries to which identified peptides were assigned. Proteins listed have at least one specific peptide that confirms the presence of the protein in the pull-down. Supplementary Table S4. Complete Millipore KinaseProfilerTM panel. For each kinase, the percent activity remaining at 1 µM and 10 µM of INNO-406 was measured. 2 Supplementary Figure Legends Supplementary Figure S1. Millipore KinaseProfiler™ Service Assay Protocols. This manual provides the screening conditions and protocols used in the KinaseProfiler radiometric protein kinase assays and HTRF® lipid kinase assays. Supplementary Figure S2. Structures of the five kinase inhibitor-unrelated drugs amphotericin B, ciprofloxacin, daunorubicin, kanamycin and paroxetine used to identify frequent hitters in K562, KU812 and chronic phase CML patient cells. Amino groups employed to immobilize each drug on the Sepharose beads (Rix, 2007) are shown in blue. The five compounds, being drugs themselves, were chosen for their properties such as size and polarity, but also for their lack of known mammalian targets (e.g. the antibiotic ciprofloxacin) or knowledge that, through coupling to the resin, binding to known targets would be disrupted (e.g. the serotonin transporter inhibitor paroxetine). The higher the incidence a certain protein is seen amongst the five experiments, the more likely it is to be a frequent hitter and selecting it as a potential target of the drug of interest should be done with caution. For the purpose of this study, we stringently subtracted all proteins identified by the negative control experiments. 3