Figure 1.
Snapshot of the simulation trajectory of wild-type MPL at 140 ns.
The gold balls represent the phosphorus atoms of the membrane bilayer. Three key residues, W491, S505, and W515, are colored red and indicated by the black arrows. The upper part of the figures is the extracellular region while the lower part the intracellular region. The tilt angle θ, demonstrated by the red arrows, defines the tilt of the transmembrane domain relative to the membrane normal.
Figure 2.
The radial distribution function (RDF, g(r) ) between water molecules and the Cβ atoms of residues 491 (upper panel), 505 (middle panel), and 515 (lower panel) of MPL.
The RDF is the distance distribution of two groups of atoms, calculated from the last 100 ns trajectory for each simulation with a sampling frequency of 10 ps, (i.e., 10,000 data points for each mutant).
Table 1.
MPL Transmembrane Domain Tilt Angles Derived from Molecular Dynamics Simulations.
Figure 3.
Effect of MPL mutations on rotation angle along the membrane axis (ie, the azimuthal angle).
Left panel: depiction of the azimuthal angle, defined as the torsion between 4 Cα atoms (red dots) of the MPL intracellular domain. The gold balls represent the phosphorus atoms of the membrane bilayer. Right panel: distribution of azimuthal angle in all simulations; the average values are indicated next to the mutant name. The distribution is calculated from the last 100 ns trajectory for each simulation with a sampling frequency of 100 ps (i.e., 1,000 data points for each mutant).
Figure 4.
Snapshots showing the conformational changes of the intracellular (IC) domain due to different mutations.
The gold balls represent the phosphorus atoms of the membrane bilayer. The MPL protein is colored green except for residues 50 to 53 (the Box1 motif, in yellow), 40 to 44 (red), 73 to 79 (blue), and 109 to 114 (white). Snapshots are taken from the simulation trajectories at 140 ns.
Figure 5.
Schematic representations of the traditional view of activation of the MPL/JAK2 signaling pathway (from A to B), and a possible alternative view derived from the current work (from A to C).
The A-to-B path shows that a ligand (thrombopoietin, TPO) binds to the extracellular (EC) domain MPL molecule, forming MPL dimers and bringing the transmembrane (TM) and intracellular (IC) domains together. The A-to-C path suggests that ligand binding changes the tilt (red arrows) and azimuthal (blue arrows) angles of the TM domain, resulting in conformational changes in the IC domains and the IC-JAK2 binding mode.