Biology Reference
In-Depth Information
The 1NEU_A model from PDB database has been used as a template
for P0 extracellular part (P0_Ex). This is a recombinant protein of rat
(Shapiro
et al
., 1996). The sequence similarity between 1NEU (rat) and the
human P0 extracellular part is very high (Fig. 2), affirming that these two
sequences are homologs and therefore must have identical 3D structure.
The theoretical pI and molecular weight of protein has been evaluated
using the Compute pI/Mw tool (Bjellqvist, 1993), available on the ExPaSy
(www.expasy.com) server. Electrostatic potential has been calculated
using the Coulomb computation method of dielectric constant (
ε=
4.0 for
protein,
80 for solvent), and using the SwissPDBViewer tool with
ionic strength of solvent 5 mM.
ε=
Amino Acid Sequence — A Basic Input for Modeling
The sequence of the P25189 entry in the UniProtKB/Swiss-Prot database
has been used as a full amino acidic sequence of human P0 protein
(Sakamoto
et al
., 1987), but the sequence denoted P25189.1 in the Swiss-
Prot database has been used as a target; in homology modeling the
“target” is the sequence whose structure is under modeling. This sequence
contains two regions: short signal region-position 1-29, and mature chain
region-position 30-248 (Fig. 1).
Multiple alignments have been calculated with the ClustalW online
tool on the EBI server using the PAM matrix and defaults for other set-
tings. The results of each pairwise alignment and the general multiple
alignment of each group of pairwise alignments with the secondary pre-
diction have been visualized using the JalView tool. The columns of
conserved residues are colored blue in Fig. 1.
Construction and Analysis of a Three-Dimensional
Atomic Model of P0 Glycoprotein
The protein part (excluding the HNK-1 epitope) of the P0 molecule (Table 1)
consists of three elements called domains: extracellular (P0_Ex), trans-
membrane (P0_TM) and intracellular (P0_Int).
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