su dhl1  (DSMZ)

Journal: bioRxiv

Article Title: Protein Interaction Screen on Peptide Matrix (PRISMA) reveals interaction footprints and the PTM-dependent interactome of intrinsically disordered C/EBPβ

doi: 10.1101/238709

Figure Lengend Snippet: A . Schematic representation of C/EBPβ and the distribution of known post-translational modifications (PTMs). Conserved regions (CRs) are depicted in colour, while intrinsic disordered regions (IDR) are shown in grey. B . Schematic description of the workflow of protein binding and data acquisition. C . Workflow of data and proteomic analysis. D . Overlap between the two replicates (SET1, SET2) of the PRISMA screen. E . Number of proteins in the two PRISMA datasets that show consecutive peptide binding (core interactions, dark amber). F . Overlap of three affinity purification-based datasets of C/EBPβ interactors as described in the literature and combined with data obtained from a proteomic interaction screen in SU-DHL1 cells. Overlaps were determined using IP SU-DHL1 as reference dataset and thus the numbers add up to the size of this set only (see Material and Methods). G . Overlap of the PRISMA-derived C/EBPβ interactor datasets from E (union of SET1 and SET2, light amber) with core interactions (dark amber) from the union of the three datasets from F (blue). Overlaps are given using the PRISMA-derived data as reference datasets. The overlap count using the union of the datasets from F as a reference dataset is denoted in brackets.

Article Snippet: Immunoprecipitation of C/EBPβ from 4×10 8 SU-DHL1 cells (anaplastic large cell lymphoma, DSMZ, ACC 356) was performed after washing twice with phosphate-buffered saline (PBS) and resuspension in lysis buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 5 mM MgCl2, 1 mM EDTA pH 8), 1 μM ZnCh 2 (Merck, Germany), 0.1% NP40 (Sigma, Germany), 2 mM dithiothreitol (DTT), 2 mM PEFAbloc (Böhringer, Mannheim, Germany) supplemented with protease inhibitor cocktail (Roche, Germany), and 20 U/ml benzonase (Sigma, Germany).

Techniques: Protein Binding, Binding Assay, Affinity Purification, Derivative Assay

Journal: bioRxiv

Article Title: Protein Interaction Screen on Peptide Matrix (PRISMA) reveals interaction footprints and the PTM-dependent interactome of intrinsically disordered C/EBPβ

doi: 10.1101/238709

Figure Lengend Snippet: Complex coverage and p-values for each of the 1432 complexes as used for the ranking of CORUM complexes ( Supplemental Information ). Each dot corresponds to one complex. Red symbols show complexes which have less than three protein hits in PRISMA and SU-DHL1 data sets. Circles represent complexes ranking within the upper quartile (dark grey) (104 complexes, dashed line between upper quartile and lower ranks), triangles encode lower-ranking complexes. The 104 highest-ranking complexes are shown in the close-up on the right. Highest-ranking complexes for each of the 14 categories from are indicated in black; other complexes which are not included in in grey.

Article Snippet: Immunoprecipitation of C/EBPβ from 4×10 8 SU-DHL1 cells (anaplastic large cell lymphoma, DSMZ, ACC 356) was performed after washing twice with phosphate-buffered saline (PBS) and resuspension in lysis buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 5 mM MgCl2, 1 mM EDTA pH 8), 1 μM ZnCh 2 (Merck, Germany), 0.1% NP40 (Sigma, Germany), 2 mM dithiothreitol (DTT), 2 mM PEFAbloc (Böhringer, Mannheim, Germany) supplemented with protease inhibitor cocktail (Roche, Germany), and 20 U/ml benzonase (Sigma, Germany).

Techniques:

Journal: bioRxiv

Article Title: Protein Interaction Screen on Peptide Matrix (PRISMA) reveals interaction footprints and the PTM-dependent interactome of intrinsically disordered C/EBPβ

doi: 10.1101/238709

Figure Lengend Snippet: A . Bar-graphs of accumulated normalised intensities for 45 selected complexes. Based on CORUM database protein complex annotations, the corresponding normalised intensities of proteins identified by PRISMA were extracted and plotted. B . Network representation of 14 potential complexes identified. Nodes are colour-coded according to their detection in PRISMA and SU-DHL1 IP experiments (yellow = detected in IP and PRISMA, green = detected in IP, dark blue = detected in the PRISMA core set, light blue = detected in PRISMA SET1 and 2).

Article Snippet: Immunoprecipitation of C/EBPβ from 4×10 8 SU-DHL1 cells (anaplastic large cell lymphoma, DSMZ, ACC 356) was performed after washing twice with phosphate-buffered saline (PBS) and resuspension in lysis buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 5 mM MgCl2, 1 mM EDTA pH 8), 1 μM ZnCh 2 (Merck, Germany), 0.1% NP40 (Sigma, Germany), 2 mM dithiothreitol (DTT), 2 mM PEFAbloc (Böhringer, Mannheim, Germany) supplemented with protease inhibitor cocktail (Roche, Germany), and 20 U/ml benzonase (Sigma, Germany).

Techniques: