Virtual Molecule: P0 Myelin Glycoprotein. I. Homology Modeling and Prediction of the Secondary and Tertiary Structure - Molecules: Nucleation, Aggregation and Crystallization - page 241

Table 1. The Theoretical Properties of the Three Parts of P0 Protein a

Peptide position P0 part MW [Da] pI

1-126 P0_Ex 14437.08 5.47

127-152 P0_TM 2758.51 8.56

153-219 P0_Int 7603.91 10.87

a The pI (isoelectric point) of the P0_Ex and P0_Int parts of the molecule is significantly different:
very low for the extracellular part (5.47) and high for the intracellular part (10.87).

14.5 kDa (Table 1). The three-dimensional structure of this domain has
been crystallized and the solved structure is deposited in RCSB (the
Research Collaboratory for Structural Bioinformatics) and PDB (Protein
Data Base) (www.rcsb.org) under 1NEU accession number (Shapiro et al .,
1996). This model has been used in research as a template for homology
modeling of the extracellular domain. There is a 97% identity between the
analyzed sequence of human P0 and the sequence of the 1NEU model
(Fig. 2).
In the 1NEU model there is one gap in the structure: the lack of infor-
mation about coordinates of segment 132 Pro- 133 Pro- 134 Asp- 135 Ile (in
mature protein without signal region: 103 Pro- 104 Pro- 105 Asp- 106 Ile). This
loop has been automatically generated by the SWISS-MODEL (Fig. 3).
The spatial structure of each model after each step of modeling has been
verified and optimized by running the Verify3D, WhatIf, Gromos and
Anolea programs.
Spatial polypeptide chain conformation and the distance from the
membrane of the P0_Ex domain have been calculated and established on
hydrophobicity and hydrophilicity profiles (Figs. 5 and 6) (Choe, 1996;
Sharpio et al ., 1996), as well as the spatial localization of peptides (Figs.
6B and 6C) known as autoimmune epitopes of myelin P0 protein (Westall,
2006) and the location of HNK-1 1 (Kirschner et al ., 1996; Sharpio et al .,
1996; Voshol et al ., 1996; Cebo et al ., 2002).

1 HNK-1 stands for human natural killer-1, it is a protein carbohydrate epitope, also known
as CD57 and LEU7.