Virtual Molecule: P0 Myelin Glycoprotein. I. Homology Modeling and Prediction of the Secondary and Tertiary Structure - Molecules: Nucleation, Aggregation and Crystallization - page 247

-helixes. That is why this confirmation has
been chosen to build the model of the whole P0 protein.
The P0_Int subunit is very flexible and movable (Fig. 7(b)) (Wong,
Filbin, 1994; Luo et al ., 2007). in the presented model the hydrophobic
domain of the P0 intracellular part is located close to the membrane, but
the charge of the whole subunit (Fig. 8; Tables 1-3) allows one to change
this orientation into the polar environment (in this case, water).

two β -strands parallel to two α

Theoretical model of P0

The final model of the whole P0 protein (Fig. 7) has been verified using
the WhatIf, Verify3D, Anolea and Gromos tools. The three-dimensional
structure of the elaborated model is correct but needs better optimization
of the torsion angles for advanced simulations.
The oligosaccharide epitope has been designed using the ChemSketch
tool and 3D models of oligosaccharide ligands of a number of models
from the Protein Data Bank (for instance, 1AC0, 2H6O and 2V82). The
composition of HNK-1, interactions with the protein and the position of
the epitope have been constructed based on the data from numerous pub-
lications (Voshol et al ., 1996; Ong et al ., 1999; Cebo et al ., 2002; Kakuda
et al ., 2004; Kleene, Schachner, 2004; Kakuda et al ., 2005) .

Hydrophobicity and Electrostatic Potential of P0 Protein

The profiles of hydrophobicity and hydrophilicity of the P0 protein are shown
in Figs. 4 and 5. There are clear sharp maxima (Figs. 5(B) and 5(D)) of the
hydrophobic and hydrophilic zones. Strongly hydrophobic residues of P0_Ex
and P0_Int are located in the central part of the molecule and are inaccessible
for environment (red residues on Fig. 6(A), 8(a) and Tables 1-3). A very sim-
ilar situation occurs in both P0_Ex and P0_Int parts; moreover, hydrophilic
residues are oriented towards the outside of the molecule. The transmem-
brane part is highly hydrophobic (Figs. 4 -7) and folded in the stable -helix.

The general electrostatic potential of the P0_Ex part contains numerous
positive and negative local charges of a short range (Fig. 8). The sources
of charge are polar amino acids. The P0_TM part consists of non-polar and

α