Binding to DPF-motif by the POB1 EH domain is responsible for POB1-Eps15 interaction-0

<p><b>Copyright information:</b></p><p>Taken from "Binding to DPF-motif by the POB1 EH domain is responsible for POB1-Eps15 interaction"</p><p>http://www.biomedcentral.com/1471-2091/8/29</p><p>BMC Biochemistry 2007;8():29-29.</p><p>Published online 21 Dec 2007</p><p>PMCID:PMC2238750.</p><p></p>er plate and incubated with the EH domain of POB1 fused to GST and GST alone as negative control. The bound domain was identified with an anti-GST antibody and a secondary antibody linked to alkaline phosphatase; wt is a phage not exposing any ectopic peptide. Below: sequences of the selected peptides are aligned with respect to the NPF and DPF motifs

Binding to DPF-motif by the POB1 EH domain is responsible for POB1-Eps15 interaction-5

<p><b>Copyright information:</b></p><p>Taken from "Binding to DPF-motif by the POB1 EH domain is responsible for POB1-Eps15 interaction"</p><p>http://www.biomedcentral.com/1471-2091/8/29</p><p>BMC Biochemistry 2007;8():29-29.</p><p>Published online 21 Dec 2007</p><p>PMCID:PMC2238750.</p><p></p>e: (A), Eps15 EH1, PDB code: (B) and POB1, PDB code: (C) EH domains. Residues in the hydrophobic groove are coloured in red, residues which line the edge of the binding pocket are in green while the gate charged residues are in blue. (B) : representation of the classical binding pocket of Eps15 EH1 domain. : residues distant from the binding pocket, which have been discussed in the text, are mapped on the molecular surface of Eps15. Lys 21 indicates the position of the binding pocket. (C) : representation of the classical binding pocket of POB1 EH domain. : residues mutated in this study are mapped on the molecular surface of POB1. Lys 307 indicates the position of the binding pocket. Lysine residues are coloured in blue, Phe344 and Ile347 in red and Gln289 in orange. Molecular surfaces were generated with PyMol

Binding to DPF-motif by the POB1 EH domain is responsible for POB1-Eps15 interaction-2

<p><b>Copyright information:</b></p><p>Taken from "Binding to DPF-motif by the POB1 EH domain is responsible for POB1-Eps15 interaction"</p><p>http://www.biomedcentral.com/1471-2091/8/29</p><p>BMC Biochemistry 2007;8():29-29.</p><p>Published online 21 Dec 2007</p><p>PMCID:PMC2238750.</p><p></p> 12 amino acids, on a cellulose membrane using the SPOT synthesis method [21]. The membrane was incubated with the EH domain of POB1 fused to the GST and probed with an anti-GST antibody. The groups of spots considered to be positives are indicated as a, b, c and d. Positives controls, binding to secondary antibodies, are indicated with rectangles. (B) Amino acid sequence of human Eps15. The N-terminal region comprising the three EH domains is underlined, sequences corresponding to the spots considered to be positives are outlined. Residues corresponding to the indicated regions are: a (aa 623–633), b (aa 647–674), c (aa 592–606) and d (aa 796–813)

Binding to DPF-motif by the POB1 EH domain is responsible for POB1-Eps15 interaction-7

<p><b>Copyright information:</b></p><p>Taken from "Binding to DPF-motif by the POB1 EH domain is responsible for POB1-Eps15 interaction"</p><p>http://www.biomedcentral.com/1471-2091/8/29</p><p>BMC Biochemistry 2007;8():29-29.</p><p>Published online 21 Dec 2007</p><p>PMCID:PMC2238750.</p><p></p>er plate and incubated with the EH domain of POB1 fused to GST and GST alone as negative control. The bound domain was identified with an anti-GST antibody and a secondary antibody linked to alkaline phosphatase; wt is a phage not exposing any ectopic peptide. Below: sequences of the selected peptides are aligned with respect to the NPF and DPF motifs

Binding to DPF-motif by the POB1 EH domain is responsible for POB1-Eps15 interaction-4

<p><b>Copyright information:</b></p><p>Taken from "Binding to DPF-motif by the POB1 EH domain is responsible for POB1-Eps15 interaction"</p><p>http://www.biomedcentral.com/1471-2091/8/29</p><p>BMC Biochemistry 2007;8():29-29.</p><p>Published online 21 Dec 2007</p><p>PMCID:PMC2238750.</p><p></p>g 10 DPF tripeptides, as described in Figure 3, were incubated with a cell extract from Hek293. Bound proteins were resolved by SDS-PAGE and analyzed by western-blotting using an anti-Eps15 antibody

Binding to DPF-motif by the POB1 EH domain is responsible for POB1-Eps15 interaction-3

<p><b>Copyright information:</b></p><p>Taken from "Binding to DPF-motif by the POB1 EH domain is responsible for POB1-Eps15 interaction"</p><p>http://www.biomedcentral.com/1471-2091/8/29</p><p>BMC Biochemistry 2007;8():29-29.</p><p>Published online 21 Dec 2007</p><p>PMCID:PMC2238750.</p><p></p>ins (EH1-EH2-EH3) were tested in a pull-down experiment from Hek293 to evaluate the relative binding efficiency towards endogenous Eps15. (B) The isolated GST-EH domains (EH1, EH2, EH3) and the N-terminal region of Eps15 were tested in a similar experiment. The input lane corresponds to 0,1% of the lysate. Relative binding efficiencies represent the quantification of the Western blotting using the Image Quant Software. In the lower panel, the GST fusions are visualized by Coomassie staining

ProtNet: a tool for stochastic simulations of protein interaction networks dynamics-2

<p><b>Copyright information:</b></p><p>Taken from "ProtNet: a tool for stochastic simulations of protein interaction networks dynamics"</p><p>http://www.biomedcentral.com/1471-2105/8/S1/S4</p><p>BMC Bioinformatics 2007;8(Suppl 1):S4-S4.</p><p>Published online 8 Mar 2007</p><p>PMCID:PMC1885856.</p><p></p>s initially seeded were varied to reach a final occupancy of 10%, 20% and 40%. Every 100 time steps the number of monomers, dimers, trimers and tetramers were counted and plotted as a function of the time steps. The figures in the ordinates represent the number of molecules at occupancy 10%. The curves for occupancies of 0.2 and 0.4 were adjusted accordingly for sake of clarity and comparison to take into account the different number of starting monomers in the grid

HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms-1

<p><b>Copyright information:</b></p><p>Taken from "HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms"</p><p></p><p>BMC Bioinformatics 2005;6(Suppl 4):S21-S21.</p><p>Published online 1 Dec 2005</p><p>PMCID:PMC1866386.</p><p></p>ntology graph induced by protein 'i ' is in green, while the one induced by protein 'j' is in blue. Dij is the number of edges that the two induced graphs have in common. B) For any given network we have derived a 'scrambled network' containing the same protein nodes linked by the same number of edges with their connections rearranged at random. For each interacting protein pair, in which both proteins have a GO annotation, we have then calculated Dij. Finally we have plotted, as a function of Dij, the difference between the percentage of nodes having a specific Dij in the inferred and in the scrambled network

ProtNet: a tool for stochastic simulations of protein interaction networks dynamics-4

<p><b>Copyright information:</b></p><p>Taken from "ProtNet: a tool for stochastic simulations of protein interaction networks dynamics"</p><p>http://www.biomedcentral.com/1471-2105/8/S1/S4</p><p>BMC Bioinformatics 2007;8(Suppl 1):S4-S4.</p><p>Published online 8 Mar 2007</p><p>PMCID:PMC1885856.</p><p></p>eins forming the Anaphase Promoting Complex (APC). The remaining graphs depict the largest complexes containing the protein CDC27 that were observed at a random specific step toward the end of the simulation (100000 steps)

HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms-2

<p><b>Copyright information:</b></p><p>Taken from "HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms"</p><p></p><p>BMC Bioinformatics 2005;6(Suppl 4):S21-S21.</p><p>Published online 1 Dec 2005</p><p>PMCID:PMC1866386.</p><p></p> Human experimental network (HEN), the Human inferred (HomoMINT) data set, the Mammalian data set in MINT and C), for a random network of similar size and for a scale-free network assembled according to Barabasi [31]