Virtual Molecule: P0 Myelin Glycoprotein. I. Homology Modeling and Prediction of the Secondary and Tertiary Structure - Molecules: Nucleation, Aggregation and Crystallization - page 245

The P0 intracellular part

This part is much smaller than P0_Int: it has a 67-a.a.-long region; MW is
7604 Da. This region is strongly hydrophilic (Figs. 4-6), of strong posi-
tive charge (Fig. 8), and has alkaline properties (Tables 1-3).
The intracellular part has been estimated and designed as a combination
of two α -helixes and two ribbons of β -strands (Wong, Filbin, 1994; Luo

et al ., 2007). One of the -strands is strongly hydrophobic (in proximity to the

190-195 region; Figs. 1 and 5). There are two possibilities for modeling this

β

Fig. 6. The space filling models A, B, C of the whole sequence of P0 protein containing
the HNK-1 epitope. (A) exhibits hydrophobic (red) and hydrophilic (blue) residues. Color
intensity represents the strength of the property (for instance, light blue means faintly
hydrophilicity; dark blue signifies strong hydrophilicity) in accordance with the Kyte,
Doolittle (1982) scale data. A special PyMOL (company name) script was written to cal-
culate the hydrophobicity profile. The strong hydrophobic transmembrane helix is colored
dark red. (B) and (C) show similar types of hydrophobicity profiles, the intense green color
meaning high hydrophilicity. The autoimmune epitops (Zou et al ., 2000; Westall, 2006)
are colored red in these two figures. In addition, on (C), both peptides are shown as
ribbons. The HNK-1 oligosaccharide is colored orange.