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Computational Molecular Biology 2015, Vol. 5, No. 1, 1-13
http://cmb.biopublisher.ca
3
Table 1 α and ß chains of hemoglobin are obtained from accessing biological database. Protein names, Access number and GeneBank
following is shown
Protein names
Access Number
GeneBank
HBA_
Camelus bactrianus
P63105
http://www.uniprot.org/uniprot/
HBA_
Camelus dromedarius
P63106
http://www.uniprot.org/uniprot/
HBA_
Camelus ferus
102513641
http://www.genome.jp/kegg/
HBA_
Homo sapiens
P69905
http://www.uniprot.org/uniprot/
HBA_
Bos taurus
P01966
http://www.uniprot.org/uniprot/
HBA_
Equus caballus
P01958
http://www.uniprot.org/uniprot/
HBB_
Camelus bactrianus
P68230
http://www.uniprot.org/uniprot/
HBB_
Camelus dromedarius
P68231
http://www.uniprot.org/uniprot/
HBB_
Camelus ferus
S9WA55
http://www.uniprot.org/uniprot/
HBB_
Homo sapiens
P68871
http://www.uniprot.org/uniprot/
HBB_
Bos taurus
D4QBB3
http://www.uniprot.org/uniprot/
HBB_
Equus caballus
F6RDD3
http://www.uniprot.org/uniprot/
Abbreviations: HBA: α-chain of hemoglobin; HBB: ß-chain of hemoglobin
1.3 Protein composition
Predicted structural classes of the whole protein were
used by Alpha Deléage & Roux Modification of
Nishikawa & Ooi 1987 (Deléage and Roux, 1987).
Protein structure, titration curves, AAs composition
and frequency of each protein were performed by the
Protean (DNASTAR Inc., Madison, WI. USA).
1.4 Prediction of protein structure
We predict tertiary structure of hemoglobin
subunits based on homology-modelling using of
SWISS-MODEL available in the ExPASy website
(http://swissmodel.expasy.org/). Which, its purpose is
to make Protein Modelling accessible to all
biochemists and molecular biologists all around the
world.
1.5 Prediction of N- and O-Glycosylation sites
In this study we utilized a new webserver GlycoEP
(http://www.imtech.res.in/raghava/glycoep/submit.htm
l) for more accurate prediction of N-linked, O-linked
and C-linked glycosylation sites of HBA and HBB or
non-enzymatic binding of glucose to the protein (as in
the case of HbA1c) in camel species and human.
1.6 Comparative modeling
In order to compute comparative modeling, we used
some criterions such as homology, conserved,
consensus and E-value by BlastP amongst mentioned
species and compare the NCBI HomoloGene database
to assign them to the gene families. Eventually,
PSI-BLAST (Position-Specific Iterated BLAST) was
done in order discovering of HomoloGene between
camel hemoglobin and various species of protein in
the chosen database (Altschul et al., 1997).
2 Results and Discussion
2.1 Multiple alignments of hemoglobin subunits:
The multiple alignments were revealed Leu, Lys, Val,
Lys, Glu, Gly, Glu, Ala, Leu, Arg, Pro, Thr, Phe, Phe,
Asp, Leu, Ser, Ala, Val, Lys, His, Gly, Lys, Val, His,
Asp, Leu, Ser, Leu, His, Lys, Leu, Val, Asp, Pro, Asn,
Phe, Leu, Leu, Leu, Ala, Phe, Thr, Pro, Ala, Lys, Val,
Leu and Tyr that these are conserved entirely in all
hemoglobin’s subunits (Figure 1). Due to the
conserved sequences it could be conjectured that the
least mutation had occurred in these kinds of AA for
mentioned species or some aa because had eliminated
by mutations that resided these conserved sequences
for hemoglobin subsequently. On the base of
conserved sequence Leu has major contribution than
others, so that according to the Binder et al., 2013,
beneficial effects of leucine on intestinal
gluconeogenesis and islets of Langerhans’s
physiology might help prevent diabetes type II
(Binder et al., 2013). Meanwhile, on the base of
Figure 1 a lot of AAs are conserved for alpha and beta
subunit of hemoglobin separately in mentioned
species, so this indicates that the least mutation has
occurred in hemoglobin structure after divergence of
species. So we can conclude that the structure of the