Thesis final - after defense-7 - Jacobs University

Chapter 3
r 2 values from the data of the three base supports were 0.90, 0.89 and 0.79 for the scales of
Miyazawa-Jernigan, Cowan-Whittaker and Tanford, respectively. It was also reported before
that the scales of Cowan-Whittaker and Miyazawa-Jernigan have provided the best correlation
for the prediction purposes in comparison to other scales (114). Although ASH is the most
precise method, but the trends observed in case of average hydrophobicity cannot be ignored.
The reason for this could be that, although amino acids on the surface are deciding for
retention, the unfolding of proteins may occur during chromatographic experiments resulting
in retention based on the total hydrophobicity of a protein.
Figure 24 A: Represents the average hydrophobicity calculated by the scale of Cowan-
Whittaker. The protein average hydrophobicity values of the three base supports were
correlated with the respective salt concentrations where the fractions were collected. The error
bars represent the standard deviations of the average hydrophobicity values in each fraction.
The statistical analysis revealed a significant correlation (r 2 = 0.89; p < 0.0001).
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