3.3.2 ǀ Subcellular localization, structure, function and
various properties of cpOAS1 protein
cpOAS1 protein is possibly multi-located but dominates in the cytoplasm
and is a soluble protein (FIGURE 4 and Table 3) based on the result of
PSORT II and DeepLoc-1.0 servers. Based on the signal peptide prediction
using SignalP 5.0 server and Signal-3L 3.0 engine, there were no signal
peptide and cleavage sites in the cpOAS1 protein (FIGURE 5SA).
Transmembrane of TMHMM results showed that there is no predicted
transmembrane helix in the sequence of cpOAS1 (FIGURE 5SB). Prediction
of the secondary structure of cpOAS1 protein by the SOPMA revealed that
the alpha helix (43.92%) is dominated followed by the random coil
(39.86%), extended strand (13.85%) and beta-turn (2.36%) and
percentage of other structures like Pi helix, Beta Bridge, Beta region,
ambiguous states, etc. were zero (FIGURE 6S). Based on NetSurfP, it was
found that the cpOAS1 protein has a combination of buried and exposed
amino acid residues (FIGURE 5). The relative surface accessibility (RSA)
value was ranged from 0.004 to 0.840 and absolute surface accessibility
(ASA) was 0.672 to 151.586. Maximum disorders residues were present at
the C-terminal end (FIGURE 5). Rossmann fold sequence domains and their
specificity for the cofactors FAD, NAD or NADP were not found in the
cpOAS1 protein (FIGURE7S). Various sequences, which show anti-oxidative
properties, were found in the cpOAS1 (Table 4).
3.3.3 ǀ Immunological features of
cpOAS1
B cell epitope prediction
(Bepipred Linear
Epitope Prediction 2.0) using IEDB analysis indicated that there are 14
potential immunogenic sites in the cpOAS1 which can act as antigen
while, with a 50% threshold, seven sites act for T cell epitope
(immunogenicity prediction) given in Table 5 and Figure 8S. The residues
with scores above the threshold (0.5) are predicted to be part of an
epitope and colored in yellow on the graph (where Y-axes depict residue
scores and X-axes residue positions in the sequence).