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Computational Molecular Biology 2014, Vol. 4, No. 14, 1-9
http://cmb.biopublisher.ca
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Model validation and optimization
The final tertiary structures of the enzymes were
visualized usigPyMol visualization tool. Then by using
PyMolvisualiser we got the number of atoms present in
all the enzymes, formal charge sum, and partial charge
sum, molecular and solvent accessible surface area. The
backbone confirmation of all the enzymes were checked
using Rampage server (mordred.bioc.cam.ac.uk/
~rapper/rampage.php) from where we got the residues
lying in allowed, favoured and outlier regions [13]. Then
the models were subjected to ANOLEA-swiss model
from where we got the Z-score, QMEAN score. The
model with least Z-score is generally selected as the best
model. The detail information is shown in Table 7.
Table 7 Backbone confirmation of all enzymes
Models
Residues in favoured region Residues in allowed region Residues in outlier region QMEAN score
Z-score
A2XNV3 92.5%
4.6%
2.9%
0.628
-1.673
Q4ADV8 94.9%
3.0%
2.2%
0.718
-0.57
Q5JLP4 92.1%
5.8%
2.1%
0.668
-1.188
Q8LNV6 91.1%
5.8%
3.0%
0.564
-2.445
Q9FUJ1 94.3%
5.1%
0.6%
0.747
-0.256
Q9FUJ3 94.0%
3.8%
2.1%
0.66
-1.284
Q67YU0 93.3%
4.9%
1.8%
0.704
-0.774
Q9T0N8 97.0%
2.4%
0.6%
0.784
0.216
Q9LY71 93.8%
4.6%
1.7%
0.69
-0.927
Q9LTS3 93.2%
4.6%
2.3%
0.676
-1.096
Result and Discussion
Sequence retrieval analysis
The amino acid sequences were successfully retrived
from uniprot, which showed the following
informations.
Multiple sequence alignment result
From the MSA analysis we got that there are many
conserved residues among all the enzymes i.e, D, F, G,
V, P, L, H, S, Q, W, Y, N, C, T, R, A, E, V, P, K, I. the
similarities are denoted with *, dissimilarities with .
and gaps with -.
Physico-chemical analysis result
From the physico-chemical analysis it is found that
the A2XVN3 enzyme of
O.sativa
has longest domain
region whereas Q9FJU3 of
A.thaliana
has smallest
domain region. The Q67YU0 of
A.thaliana
has
highest molecular weight, A2XVN3 enzyme of
O.sativa
has highest theoretical PI and aliphatic index,
Q4ADV8 enzyme of
O.sativa
has highest total
number of atoms.
Secondary structure prediction result of all
enzymes
The secondary structures of all the enzymes were
predicted using CFFSP server from where we could
got the percentage of alpha, helix, turns. The helix is
denoted with red colours, sheet is denoted with green
colours, turn is denoted with blue colours. The
secondary structures of all the enzymes are given from
Figure 2-Figure 11.
Homology modeling results
The models which were generated by using phyre2
server were visualized by using PyMol visualization
tool, which showed the following result.
Backbone confirmation result of enzymes
The final generated models of all the enzymes were
submitted to RAMPAGE server from where we got
the residues lying in allowed, favoured and outlier
regions. The detail information is given below.
Discussions
From the above study we got the functions of all the
enzymes, the most common residues among them,
from the physico-chemical analysis we got that
A2XVN3 of
O.sativa
has the most longest domain
region. The best model which was selected on the
basis of Z-score was Q8LNV6 of
O.sativa
. All the
enzymes has most common domain i.e, FAD binding
PCMH type. Depending upon the back-bome
confirmation of enzymes the best model was Q9T0N8