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Computational Molecular Biology 2014, Vol. 4, No. 15, 1-5
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2.2 Alignment between domain region and whole
enzyme
The domain region was extracted from the whole
protein sequence and subjected to clustalw2 for
multiple sequence alignment. From this study the
conserved residues among domain region and whole
enzyme sequence were obtained. The match regions
were denoted with *, mis-match regions with . and the
gaps were denoted with -. Here the Figure 1 shows the
common residues.
2.3 Homology modeling analysis
The homologous models for both enzyme and domains
were generated. The helices are denoted red colours,
helices with yellow colours and the loops are denoted
with green colours respectively. The VDW radius, beta
factor, mass of structures, stability of the objects were
found from yasara tool. Then total number of atoms,
formal charge sum, molecular surface area and solvent
accessible surface area were found from pymol tool.
2.4 Model validation and optimization
The backbone confirmations of the structures were
generated from rampage server. 91.8% of the residues lie
in most favored region whereas 3.3% of the residues lie
in outlier region. The QMEAN score and Z-scores were
found from both anolea server and from prosa server
.
2.5 Active site analysis result
The active sites were found from castp server. The
balls with green color show the binding regions of
whole protein and the domain region. Many pockets
were found, but out of them the first volume was
selected. The pockets of domain were mainly ALA,
ARG, CYS, HIS, GLY, VAL, SER, TYU, LEU, PHE,
ILE, THR, PRO and similarly the pockets of whole
enzyme were PHE, ILE, LEU, VAL, SER, HIS, GLY,
CYS, ALA, MET, GLU, THR, ASP, TYR, ASN, GLN,
PRO, TRP, GLN respectively.
2.6 Protein-ligand interaction
The pdb files of protein, domain and the ligand were
submitted and by adding polar hydrogens to protein
and domain the interaction was studied. The binding
energy which was found between the interactions of
whole protein-ligand (FAD) was -11.23, with -14.81
intermolecular energy, 3.58 torsion energy and 13.66
internal energy. Similarly the interaction which was
performed between the domain region and ligand
(FAD) showed -10.91 binding energy, -14.49
intermolecular energy, 3.58 torsion energy and 14.04
internal energy respectively.
From the interaction it is found that the FAD is
binding to ALA6, ARG1, AR536, TYR10, ASP55,
ALA57, CYS38 at the domain part and in whole
protein the domain is binding to ARG134, ASP128,
SER131, TYR83, SER85, LEU135, ARG86, GLN136,
LEU135, LEU47.
3 Discussions
From the above study it is found that the model of whole
enzyme and the domain are suitable for future analysis as
most of the residues lie in favored region. The main
objective of this study was to find the stronger interaction
of ligand (FAD) with the domain part of enzyme and
with the whole sequence, which showed that the binding
interaction is stronger between the domain part and FAD
than in comparison to the interaction between FAD and
whole amino acid sequence
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