Virtual Molecule: P0 Myelin Glycoprotein. I. Homology Modeling and Prediction of the Secondary and Tertiary Structure - Molecules: Nucleation, Aggregation and Crystallization - page 248

Fig. 7. (A) Ribbon model of P0 protein and possible arrangement relative to a lipid bilayer.
(B) The space filling model of the whole P0 protein anchored in lipid bilayer. Higher intensity
of green indicates more hydrophilicity. The HNK-1 epitop is colored orange. The surface of the
membrane is covered by a narrow band of water (blue). (A) shows the ribbon/cartoon model
of the protein part of P0 colored in accordance with the Kyte, Doolittle (1982) hydrophobicity
scale (red for hydrophobic, blue for hydrophilic). The model of the HNK-1 epitop is shown as
Van der Waals (VDW) spheres colored according to the type of atom (carbon is colored white;
oxygen is colored red; sulfur is colored yellow; nitrogen is colored blue). The VDW model
(a type of model where each atom is represented by a sphere at the center of the atom and the
radius of sphere is equal to the Van der Waals radius, the range of Van der Waals interactions)
illustrates the space occupied by the molecule in natural circumstances. The orientation of the
P0_Ex head is estimated from published data (Westall, 2006; Jeremy, 2001; Shapiro et al .,
1996; Choe, 1996; Kirschner et al ., 1996; Luo et al ., 2007). The 28 Trp interacts with the sur-
face of the next membrane and its aromatic rings are flat/parallel to the membrane surface. The
distance between the next two lipid bilayers is about 46 Å (Shapiro et al ., 1996) and it is almost
equal to the height of the P0_Ex subunit. The HNK-1 epitop stabilizes the spatial orientation
of the extracellular head of protein linked by a single flexible coil to the transmembrane helix.
The intracellular part of the P0 protein is also linked by the single long and dynamic loop to the
membrane part of protein and this joint is not stabilized. In addition, the P0_Int part is highly
charged (Fig. 8) and movable (Fig. 7B) (Wong, Filbin, 1994; Luo et al ., 2007). The movability
of the P0_Int part is depicted as X, Y, Z positions (green, blue and red) with arrows.