11 research outputs found
MOESM2 of Efficient conformational sampling and weak scoring in docking programs? Strategy of the wisdom of crowds
Additional file 2: Table S1. Table gathering the results of docking and protein and ligand properties. The target name from DUD-E is given in column A. The difficulty of docking and ranking, column B, is colored in green for the 28 easy targets (top-ranked with all programs), in red for the 6 hard targets (with no correct best pose found with any program), in pink for the 9 best but not top-rank targets exposed in Table 5 (a correct best pose found by at least one program but not top-ranked with any scoring function when rescored in one pool). The rest is in gray. The protein properties are given in columns C to G and the ligand properties in columns H to O. Then follow the RMSDs of the top-rank and best poses obtained when docking with Glide (columns P, Q), Surflex (R, S), FlexX (T, U) and Gold (V, W)
MOESM1 of Efficient conformational sampling and weak scoring in docking programs? Strategy of the wisdom of crowds
Additional file 1: Four supplementary figures. They show the distribution of the protein (Figure S1) and small molecule (Figure S2) properties, the comparison of two scoring functions of Gold and Glide for docking and rescoring (Figure S3) and finally, the comparison of the properties for easy and hard targets (Figure S4)
MOESM1 of Benchmark of four popular virtual screening programs: construction of the active/decoy dataset remains a major determinant of measured performance
Additional file 1. All Tables and Figures of the Additional file
MOESM1 of vSDC: a method to improve early recognition in virtual screening when limited experimental resources are available
Additional file 1. The additional file contains all the supplementary material, i.e. five Figures and one Table
Crystal structure of the β-catenin/ICAT complex.
<p><b>A</b> Crystal structure of ICAT bound to the core domain of β-catenin (PDB code 1LUJ,[<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0172603#pone.0172603.ref022" target="_blank">22</a>]). ICAT is shown as yellow ribbons and β-catenin as purple cylinders. The secondary structures were calculated using the program STRIDE [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0172603#pone.0172603.ref037" target="_blank">37</a>]. Residues mutated in this study are shown as hard spheres. ICAT residues are colored according to their characteristics: white for hydrophobic, green for polar, red for acidic and blue for basic residues. β-catenin F660 is in pink and the basic residues facing the C-terminal domain of ICAT are in cyan. <b>B</b>. Sequence alignment of the consensus peptide from several β-catenin binding proteins. The conserved acidic residues are in red and the aromatic residue in green. The first X residues, when they are hydrophilic, are boxed. <b>C</b>. β-catenin/ICAT complex showing the interaction between ICAT consensus peptide of the C-terminal domain (ribbon and sticks) and its facing β-catenin residues (surface). All residues are colored according to their characteristics. Figures were drawn using VMD software [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0172603#pone.0172603.ref038" target="_blank">38</a>].</p
The lack of helix C in β-catenin does not prevent interaction with ICAT.
<p><b>A</b>. Schematic representation of WT and mutant Δ665 HA-tagged β-catenin-NLS proteins. <b>B</b>. Total cell lysates from Lu1205 cells transfected with WT or mutant β-catenin Δ665 were analyzed by WB or affinity immunoprecipitated with WT ICAT-GST recombinant protein and blotted with anti-HA and anti-ICAT antibodies. Numbers represent mean ± SD of normalized densitometry values from three independent experiments, *p<0.05.</p
ICAT negatively regulates the M-MITF promoter activity by competing with LEF1.
<p><b>A.</b> Mel501 cells were transfected with a <i>M-MITF</i>::<i>luciferase</i> vector in the presence of increasing amounts of <i>CMV</i>::<i>ICAT-WT</i> expression vector. Data are presented as means ± SEM of three independent experiments. <b>B.</b> qRT-PCR analysis of <i>M-MITF</i> mRNA levels in Mel501 cells transfected with empty or <i>ICAT-WT</i> expression vectors. <b>C.</b> WB analysis of MITF and ICAT proteins in Mel501 cells transfected with empty or <i>ICAT-WT</i> expression vectors. <b>β</b>-actin = loading control. <b>D.</b> WB analysis of MITF and p27<sup>Kip1</sup> protein levels in siRNA and ICAT-transfected Mel501 cells. SiMITF treatment and ICAT overexpression induce respectively a 42% and 35% increase of p27 protein amount; Scrb = control scrambled siRNA. <b>E</b>. Mel501 cells were transfected with <i>M-MITF</i>::<i>luciferase</i>, <i>LEF1</i> and <i>ICAT-WT</i> expression vectors. Data are presented as means ± SEM of three independent experiments. *p<0.05, **p<0.01, ***p< 0.001; ****p<0.0001.</p
List of ICAT and β-catenin mutants created by site directed-mutagenesis.
<p>List of ICAT and β-catenin mutants created by site directed-mutagenesis.</p
Interactions between ICAT and β-catenin mutants, K312E, K435E and R386G in Lu1205 cell extracts: Consequences on <i>NEDD9</i> promoter activity.
<p><b>A</b>. Left: WB analysis of lysates (Input) from Lu1205 cells transfected with WT or mutant HA-tagged β-catenin constructs; right: Pull-down assay of HA-tagged WT and mutant β-catenin (K312E, K435E and R386G) by WT ICAT-GST recombinant protein. <b>B</b>. Left: WB analysis of lysates (Input) from Lu1205 cells transfected with WT or mutant HA-tagged β-catenin constructs; right: Pull-down assay of HA-tagged WT and mutant β-catenin (K312E and K435E) by LEF1-GST recombinant protein. <b>C</b>. Lu1205 cells were transiently transfected with <i>NEDD9</i>::<i>luciferase</i> and either <i>β-catenin-WT</i> or <i>β-catenin</i> mutants <i>(K312E</i>, <i>K435E and R386G)</i> expression vectors. <b>D</b>. Lu1205 cells were transiently transfected with <i>NEDD9</i>::<i>luciferase</i> vector in the presence of <i>CMV</i>::<i>LEF1</i>. Cells were also transfected with <i>β-catenin-WT</i> or <i>β-catenin</i> mutants <i>(K312E</i>, <i>K435E and R386G)</i> expression vectors. Data are presented as means ± SEM of three independent experiments. *p<0.05, **p<0.01, ***p<0.001, ns = not significant.</p
The characteristics of the first X residue in the consensus peptide of several β-catenin binding proteins regulate their interactions with β-catenin.
<p><b>A</b>. Zoom is made on the first conserved Aspartate residue of the consensus peptide and its adjacent non conserved residues (shown as sticks) in ICAT, LEF1, TCF4, APC and E-cadherin (yellow ribbons) and the facing β-catenin Arm repeats 8 and 9 (purple cylinders). The first X residue of the consensus is encircled because residue numbering diverges between various β-catenin regulators, although they are facing the same β-catenin residues forming a basic patch. Hydrogen bonds between basic β-catenin residues and their counterpart in β-catenin regulators are presented as black dotted lines. In ICAT, V67 does not establish any hydrogen bond, whereas in LEF1 and TCF4/TCF7L2, E20 and E17, respectively make an H-bond with the facing β-catenin K508. In APC and E-cadherin, T1487 and S675 respectively form hydrogen bonds with the facing β-catenin R469. The color scheme of stick residues based on their characteristics is the same as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0172603#pone.0172603.g001" target="_blank">Fig 1</a>. PDB codes: ICAT (1luj), LEF1 (3ouw), TCF3/TCF7L1 (1g3j), TCF4/TCF7L2 (1jdh), APC (1t08) and E-cadherin (1i7w).</p