Biomedical Engineering Reference
In-Depth Information
between collagen with AA, AUTODOCK software has been used and AutoDock 4.2
used to calculate (Morris et al., 2009) the free energy of binding between the AA and
collagen. Results on binding energy calculations based on bioinformatics tools for the
cross-linking of Type-I, Type III collagen with AA using AutoDock software
(Figure
5(a),
5(b) and
6(a), 6(b))
and, Table 2,
3
depicts the values for the binding energy, in-
teraction sites, hydrogen bond sites, and bond distance of Type I and Type III collagen
respectively.
In AACC 1, the binding energy of -7.28 was observed when Ala (11) residue of
A chain of collagen interacting with AA through Nitrogen of alanine and forming
three hydrogen bond with bond distance of about 3.08, 2.97, and 2.92. Glycine (7) of
C chain of collagen interacted with AA through oxygen (of -OH group) and forming
three hydrogen bonds with the bond distance of 3.98, 2.67, and 2.55. Similarly Serine
(9) of C chain of collagen also forms one hydrogen bond through Nitrogen with bond
distance of 3.15.
table 2.
Interaction sites, binding energy, hydrogen bond sites, and bond distance, calculated based
on the bioinformatics tool for the cross-linking between collagen (Type I) and alginic acid.
Interaction site
Binding energy
(kcal/mol)
H-bond
Bond distance (Å)
Thirteenth residue Gly of A-
chain (α
1
)
-6.0
Gly A 13-(C
α
)-O
H-O(AA)
3.13
Fifteenth residue Ala of A-chain
(α
1
)
Ala A 15-(C
α
)-N
H-O(AA)
2.88 & 2.89
Thirteenth residue Gly of A-
chain (α
1
)
-6.17
Gly A 13-(C
α
)-O
H-O(AA)
2.91 & 2.62
Eleventh residue Ala of B-chain
(α
1
)
-6.31
Ala B 11-(C
α
)-N
H-O(AA)
2.83 & 3.11
Tenth residue Gly of A-chain
(α
1
)
Gly A 10-(C
α
)-O
H-O(AA)
2.61 & 3.39
Seventh residue Gly of C-chain
(α
2
)
-6.51
Gly C 7-(C
α
)-O
H-O(AA)
2.44
Eleventh residue Ala of A-chain
(α
1
)
Ala A 11-(C
α
)-N
H-O(AA)
3.17
Eleventh residue Ala of A-chain
(α
1
)
-7.28
Ala A 11-(C
α
)-N
H-O(AA)
3.08,2.97 & 2.92
Seventh residue Gly of C-chain
(α
2
)
Gly C 7-(C
α
)-O
H-O(AA)
3.98,2.67 & 2.55
Nineth residue Ser of C-chain
(α
2
)
Ser C 9-(C
α
)-N
H-O(AA)
3.15
In the case of AACC 3, binding energy of -7.14 observed when Alanine (11) resi-
due of A chain of collagen interacting with AA through Nitrogen of alanine and form-
ing three hydrogen bond with bond distance of about 3.29, 3.04, and 2.85. Alanine (9)
of C chain of collagen interacted with AA through oxygen (of -OH group) and form-
ing two hydrogen bonds with the bond distance of 3.54 and 2.78. Similarly glycine
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