Virtual Molecule: P0 Myelin Glycoprotein. I. Homology Modeling and Prediction of the Secondary and Tertiary Structure - Molecules: Nucleation, Aggregation and Crystallization - page 243

The P0 transmembrane segment is 21 amino
residues long

The transmembrane region has been estimated using SOSUI prediction
(Fig. 4), JPred, JNetHMM and SWISS-MODEL predictions (Fig. 1), and
hydrophobicity and hydrophilicity profiles (Fig. 5). Finally, the region
from 130 Gly to 151 Arg has been selected as the most probable transmem-
brane region and has been modeled as a strongly hydrophobic transmem-
brane -helix.

P0_Ex and P0_TM parts are linked by a 9-a.a.-long coil; 119 Glu … 127 Val.
This region has been generated using the Swiss-Model loops database.
Modeling uncovered the 119 Glu … 127 Val loop and three anchor positions
(immovable residues): 119 Glu as a beginning of the loop, 127 Val as an end
of the loop and 121 Val as a unique hydrophobic position in the loop. The
121

α

Val residue has been localized in the direct vicinity of the membrane
surface (Figs. 5 and 8).

Fig. 4. The results of transmembrane region prediction using the SOSUI tool. The algo-
rithm found only one 23-a.a.-long transmembrane region. It was the first step in the pre-
diction of the secondary structure domains. The algorithms calculating the hydropathy
profiles are accurate for this research.