Fig 1.
Structure of the STAT proteins.
(A) STATs structure is composed of a N-terminal domain (N-term), a Coiled-Coil domain (CCD), a DNA Binding domain (DBD), a Linker domain (LD), a SRC homology 2 domain (SH2), a Phosphotyrosyl Tail (p-Tail), and a C-terminus named the Trans-Activation Domain (TAD); (B) The crystallographic or NMR data (Protein Data Bank, PDB) characterized a structure of STAT1 (1BF5 [12], 1YVL [13] and 2KA6 [14]), STAT2 (2KA4 [14]), STAT3 (1BG1 [15], 3CWG [16] and 4E68 [10]), STAT4 (1BGF [17]), STAT5a (1Y1U [18]) and STAT6 (1OJ5 [19]). Different STATs domains are distinguished by color: N-terminal is in orange, CCD is in blue, DBD is in red, LD is in green, SH2 is in yellow, p-Tail is in grey and TAD is in magenta.
Fig 2.
(A) Topology of the STAT5 core fragment; (B) Ribbon diagram of STAT5 structure, the phosphotyrosine residue is shown in balls and sticks. Different protein domains are distinguished by color: CCD is in blue, DBD is in red, LD is in green, SH2 is in yellow and p-Tail is in grey.
Fig 3.
Molecular dynamics simulations of STAT5 proteins.
(A) The root mean square deviations (RMSDs) from the initial coordinates computed on the Cα atoms for trajectories 1 (solid lines) and 2 (dashed lines) of MD simulations. The non-phosphorylated and phosphorylated (p-) states of proteins are distinguished by color: STAT5a and p-STAT5a are in blue and in yellow (top panel), STAT5b and p-STAT5b are in green and in magenta, respectively (bottom panel). (B) The root mean square fluctuations (RMSFs) computed on the Cα atoms over the simulation time of STAT5a (STAT5a is in blue and p-STAT5a is in yellow) were compared to those of STAT5b (STAT5b is in green and p-STAT5b is in magenta). Insert: The average conformation for STAT5a is presented as tubes. The tube size is proportional to the by-residue atomic fluctuations computed on the Cα atoms. The high fluctuation regions are specified by color ranged from red to yellow and numbered from 1 to 7.
Fig 4.
Secondary structure in STAT5 proteins.
Secondary structure assignments for the STAT5 proteins were averaged over the two replicas of MD simulations. For each residue, the proportion of secondary structure type is given as a percentage of the total simulation time and shown with lines of different color: α-helix is in red, 310-helix is in black, β-sheet is in green, and β-bridge is in blue. The STAT5 structural domains are indicated at the top by a colored line (the CCD in blue, the DBD in red, the LD in green, the SH2D in yellow and the C-term tail in grey).
Fig 5.
Comparison of the global dynamics by Normal Modes Analysis of STAT5 proteins.
(A) The Cα atoms root mean square fluctuations as a function of residue number. Results for the two first modes are shown at top and bottom panels respectively, are denoted by color: STAT5a is in blue, pSTAT5a is in yellow, STAT5b is in green and p-STAT5b is in magenta. (B) First and second slowest motion modes illustrating atomic motions of STAT5a (top) and STAT5b (bottom). The STAT5 proteins displayed in cartoon representation are in light blue (STAT5a) and in dark blue (p-STAT5b). The atomic (Cα) components of each mode are drawn in red (first mode) and yellow (second mode) arrows. The length of arrows is positively correlated with motion magnitude and their orientation indicates motion direction. (C) Overlaps between the ten slowest modes of the phosphorylated and non-phosphorylated STAT5a (left) and STAT5b (right) are shown in the heatmap.
Fig 6.
Inter-residue cross-correlations maps resulting from NMA (left column) of STAT5a/p-STAT5a (top) and STAT5b/p-STAT5b (bottom). Each protein is presented in the lower and upper half-matrix, respectively. Dynamical cross-correlations for the Cα atom pairs of STAT5a, STAT5b, p-STAT5a and p-STAT5b obtained from two MD trajectories (middle and right columns). Each replica, 1 and 2, is presented in the lower and upper half-matrix, respectively. Correlated (positive) and anti-correlated (negative) motions between atom pairs are presented as color gradient of red and blue, respectively.
Fig 7.
Independent Dynamic Fragments identified in STAT5 proteins.
Top: 3D structural mapping of the Independent Dynamic Fragments (IDSs) in STAT5a referred to as Si, where i = 1, 2 …N, is presented on the average conformation as they were found by LFA (A) and by PFD (B) algorithms. Bottom: (C) Graph representation of IDSs found by PFD and LFA in each studied STAT5. Each color specifies an IDS obtained from a seed (LFA) or a predictor (PFD); the IDSs localized on the same structural fragment in various STAT5s may be colored differently according to a number of the first predicted residue in a given IDS.
Fig 8.
(A) Global inter-residue communication represented as 2D interaction networks. Residues are presented by points, communications pathways are depicted by lines. Residues are colored according they communication efficiency (CE), estimated as the number of residues connected by at least on CP, from blue (poor CE) through green and yellow to red (high CE). (B) 3D structural mapping of the inter-residue communication in STAT5. For each protein, non-phosphorylated and phosphorylated, the average MD conformation is shown as a carton. Communication pathways between residues are depicted as connected tips. The STAT5 secondary structures are labeled. Specific tyrosine is denoted as a grey ball.
Fig 9.
Pockets detected at the STAT5 surface.
(A) Two pockets (brown contours) are located in LD (in green) and SH2 (in yellow) domains; the key residues, K600, R618, S620 and S622, are shown as sticks. (B) Sequence conservation (+)/variability (-) between STAT5 and other STAT proteins. (C) The pockets volume was monitored over MD simulations of each STAT5. STAT5a is in blue, pSTAT5a is in yellow, STAT5b is in green and p-STAT5b is in magenta. The two replicas, 1 and 2, for each protein are distinguished by solid and dashed lines, respectively.
Fig 10.
Communication pathways and pockets detected in STAT5 proteins.
The Q205 –F646 “shortest” intramolecular communication pathway of each protein is superposed and shown together with the pockets on a carton representation of phosphorylated STAT5a. Phosphotyrosine is presented as sticks. Communication pathways between residues are depicted as connected color tips–blue in STAT5a, yellow in p-STAT5a, green in STAT5b and magenta p-STAT5b. Residues involved in more than one Q205 –F646 “shortest” intramolecular communication pathway are depicted as multicolor balls. The pockets P1 and P2 are shown as contoured meshes. The STAT5 secondary structures labels are shown.