Computed scaled feasibility measures using 10.0 bps/turn DNA.

<p>Computed scaled feasibility measures using 10.0 bps/turn DNA.</p

Molecular Models of STAT5A Tetramers Complexed to DNA Predict Relative Genome-Wide Frequencies of the Spacing between the Two Dimer Binding Motifs of the Tetramer Binding Sites - Fig 5

<p>Computed scaled feasibility measures of the tetramer formation vs. CTCD using two NDDs (<b>A</b>) or at least one NDD (<b>B</b>). The red and blue points are for the ‘eclipsed’ and the ‘staggered’ tetramers, respectively, with the NDD off- and on-axis, respectively. The red and blue points were scaled so as to put them on the same scale as the experimental counts (shown in thin blue line) of tetramer binding sites in the mouse genome. For this figure, we used the DNA with 10.5 bps per helical turn. The results using the 10.0 bp DNA are given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0160339#pone.0160339.g006" target="_blank">Fig 6</a>.</p

A flow chart of the model building procedure.

<p>A flow chart of the model building procedure.</p

Computed probability sums and raw feasibility measures using 10.0 bps/turn DNA.

<p>Computed probability sums and raw feasibility measures using 10.0 bps/turn DNA.</p

Computed probability sums and raw feasibility measures using 10.5 bps/turn DNA.

<p>Computed probability sums and raw feasibility measures using 10.5 bps/turn DNA.</p

Two examples of the modeled tetramer structure.

<p>Left panels (NDD on-axis): The plan view (<b>A</b>) and elevation (<b>B</b>) of the tetramer model at the CTCD of 16; the horizontal white line is the 2-fold symmetry axis. Right panels (NDD off-axis): The plan view (<b>C</b>) and elevation (<b>D</b>) of the tetramer model at the CTCD of 21; the 2-fold axis is vertical in (C) and along the viewing direction in (D). In each panel, DNA is white; the core monomers are green (core A), blue (core D), magenta (A’), and red (D’); and NDDs are yellow. The linkers between the C-terminals of the NDD and the N-terminals of the core are indicated as dotted yellow lines.</p

The domain structure of STAT proteins.

<p><b>(A)</b> Names and positions of the six domains on the primary sequence: NTD (N-terminal domain), CCD (4-helix bundle coiled-coil domain), DBD (DNA-binding domain), LD (linker or connector domain), SH2, and TAD (transactivation domain). We treated the DBD and LD as one combined domain, as SCOP [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0160339#pone.0160339.ref017" target="_blank">17</a>] does for STAT3β. There is a short flexible 13-residue linker between the NTD and CCD, which partly overlaps with the NTD. There is also a phospho-tyrosine containing segment (PTS) between the SH2 and TAD, which we combined with the TAD. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0160339#sec004" target="_blank">Methods</a> for more detail. (<b>B)</b> The sequence of mouse STAT5A (NCBI Accn# CAA88419.1). The residues are highlighted according to the domains to which they belong, using the same coloring scheme used in (A). The 13-residue linker is boxed. The phospho-tyrosine residue (Y694) and the two following residues (V695 and K696) are shown in red. <b>(C)</b> STAT5A domains in the modeled structure of the STAT5A core, which includes the CCD, DBD, LD, SH2 and the residues 694–696 of the PTS. Dotted line represents the connecting residues (685–693) that were not included in the model.</p

Histograms of the end-to-end distances of 13-residue peptides in protein structures in PDB, using only those peptides with the Blosum62 score greater than 8 (blue), 9 (red) or 10 (green) when compared to the linker sequence (shown in Box in Fig 1B) in STAT5A.

<p>Histograms of the end-to-end distances of 13-residue peptides in protein structures in PDB, using only those peptides with the Blosum62 score greater than 8 (blue), 9 (red) or 10 (green) when compared to the linker sequence (shown in Box in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0160339#pone.0160339.g001" target="_blank">Fig 1B</a>) in STAT5A.</p

STAT5 phosphorylation in Stat5b transgenic mice.

<p>(A) Representative Western blotting analysis for phosphorylated and total STAT5 in F1 and NOD Stat5b transgenic lines. These mice did not have detectable signs of lymphoma based on physical examination and FACS analysis of T cell phenotypes. Protein extracts from thymus were used for the experiment. (B) Representative Western blotting analysis of phosphorylated STAT5 with thymus protein extracts from NOD.Stat5b transgenic mice with lymphoma. (C) STAT5 phosphorylation status in different cell types. Thymocytes and splenocytes from NOD Stat5b^Tg mice were analyzed by intracellular staining for phosphorylated STAT5 with an anti–pTyr694-STAT5 antibody. (D) FACS analysis showing progressive increase of STAT5 phosphorylation in thymocytes of NOD.Stat5b^Tg mice. Data for thymus are shown here for 6, 12 and 16 week old NOD.Stat5b^Tg mice (all without tumor). Representative data are shown from 1 of 3 similar experiments.</p

Lymphoblastic lymphoma in Stat5b transgenic mice.

<p>(A) Progression of lymphoma observed in the B6xNOD F1.Stat5b^Tg mice and NOD.Stat5b^Tg mice with or without chemoprevention treatment. The lymphoma incidence is significantly different between F1 mice and NOD.Stat5b^Tg mice (p<0.001). (B) Overview of a mouse that has enlarged thymus, spleen, and lymph nodes (left panel). Enlarged spleen (SP), cervical lymph node (CN) and thymus (Thy) are compared to littermate controls (right panel). **, p<0.01, compared with that of littermate controls. (C) H&E staining of spleen, cervical node and thymus from a NOD.Stat5b^Tg mouse with lymphoma and its littermate control (LMC). Scale bars represent 50 um.</p