Chemistry Reference
In-Depth Information
Table 11.2 The solvent accessible surface area (SASA) of -Lg's oxidatively labile
amino acid residues calculated using the program GETAREA (Fraczkiewicz and Braun,
1998). The ratio of side-chain surface area to random coil value of each amino acid
residue is listed in the 4th column. The `random coil' value of a residue X is the average
solvent-accessible surface area of X in the tripeptide Gly-X-Gly in an ensemble of 30
random conformations. Residues are considered to be solvent exposed if the side-chain
surface area to random coil value ratio value exceeds 50% and to be buried if the ratio is
less than 20% (Fraczkiewicz and Braun, 1998). Buried residues are denoted with an `i'.
Cys residues in bold typeface represent residues involved in disulfide bonds (i.e. cystine).
A probe radius of 1.4
Ê
was used
Residue
Sidechain
Random coil
Ratio (%)
Buried
Met 7
25.58
158.3
16.2
X
Trp 19
0.00
224.6
0.0
X
Tyr 20
53.55
193.1
27.7
Met 24
0.00
158.3
0.0
X
Tyr 42
16.58
193.1
8.6
X
Trp 61
93.04
224.6
41.4
Cys 66
10.51
102.3
10.3
X
Phe 82
1.58
180.1
0.9
X
Tyr 99
35.28
193.1
18.3
X
Tyr 102
13.81
193.1
7.2
X
Phe 105
16.40
180.1
9.1
X
Cys 106
2.45
102.3
2.4
X
Met 107
7.34
158.3
4.6
X
Cys 119
0.15
102.3
0.1
X
Cys 121
0.00
102.3
0.0
X
Phe 136
0.10
180.1
0.1
X
Met 145
15.17
158.3
9.6
X
His 146
43.60
154.6
28.2
Phe 151
12.67
180.1
7.0
X
Cys 160
12.38
102.3
12.1
X
Adapted from Elias et al. (2008).
amino acids with antioxidant potential may be buried within the protein's
hydrophobic core where they are inaccessible to aqueous prooxidants and
radical species. For example, in native -lactoglobulin (-Lg), the majority of
free radical scavenging amino acids are located in the protein interior and
therefore may not be able to contribute to the protein's overall antioxidant
activity. The solvent accessibility of the major free radical scavenging amino
acids in native -Lg are shown in (Table 11.2), which was calculated using an
algorithm for determining solvent accessible surface area based on the protein's
crystal structure (Elias et al., 2007; Fraczkiewicz and Braun, 1998). Based on
this native structure, 17 of -Lg's most oxidatively labile amino acids are not
solvent accessible, whereas histidine 146, tyrosine 20, and tryptophan 61 are
partially exposed. On this basis, it can be argued that these amino acids are
unlikely to contribute to -Lg's overall antioxidant activity when the protein is
in its native state.
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