Virtual Molecule: P0 Myelin Glycoprotein. I. Homology Modeling and Prediction of the Secondary and Tertiary Structure - Molecules: Nucleation, Aggregation and Crystallization - page 240

Fig. 1. The multiple alignments of a few sequences of P0 protein of vertebrates. The
human P0 sequence is a reference (top) and is written on an orange background. The most
conserved residues are marked in blue (columns) and the degree of conservation is quan-
titatified in the “Conservation” row. Yellow means residues are conserved; dark yellow
means they are not. The “Swiss-model,” “jnetpred” and “JNETHMM” rows present the
results of the secondary structure predictions of each tool and method. The epitops caus-
ing experimental autoimmune neuritis (EAN) (Westall, 2006; Sedzik, 2008) are marked in
the “peptides” row. The “Quality” row presents quality of alignment — the quality of the
fit of each residue. The “Quality” row is adequate to the “Conservation” row. The diagram
in the “Consensus” row describes the accuracy of the consensus sequence estimation and
the level of variability of each residue. Higher bars in the “Consensus” row mean more
conserved residue; lower bars mean more variable position. The region adequate to the
1NEU model is marked with a pale row (region 1-119). The multiple alignments were cal-
culated using the ClustalW tool on the EBI online service. The presentation of the results
of alignment was prepared using the JalView tool.
The P0 extracellular domain — Soluble part
The extracellular domain (positions 29-147) is defined in Pfam as the
immunoglobulin V-set domain (acc: PF07686). It is the biggest part of
the P0 protein: 126 animo acids, and a theoretical molecular weight of