Thesis final - after defense-7 - Jacobs University

Chapter 3
Table 15: Average protein properties for their correlation with retention time and the ability to
differentiate among the base support for their hydrophobicity.
Protein properties
Differentiation
Correlation
Average hydrophobicity × +
Average polarity ×
_
Average flexibility × +
Average bulkiness × ×
Average surface hydrophobicity Trend +
+ indicates positive correlation, - indicates negative correlation; × indicates no correlation
These results revealed that protein properties have a limited ability to differentiate among the
base supports for their hydrophobicity. At any specific fraction of time, several proteins are
supposed to be eluted during chromatographic separation of a cell proteome. Due to this
reason, assigning a specific retention time to any protein is impractical. This revealed that the
proteome wide approach has a limited ability to differentiate among the base supports.
In two cases (1.6 M and 0 M), the Sepharose-Phenyl has given slightly high hydrophobic
proteins than Toyopearl-Phenyl. This unexpected behavior of Sepharose-Phenyl was also
reported before; where proteins with high ASH were eluted earlier than those with lower ASH.
The reason could be the heterogeneous distribution of hydrophobic hotspots on the
Sepharose-Phenyl, due to which an unusual behavior was reported in the retention mechanism
(63). Another observation was that base supports revealed less differences at high salt
concentrations than at low salt concentrations. In other words, the differences among the base
supports were less at high hydrophobic conditions than at low hydrophobic conditions. This
kind of behavior was also reported in our group with model proteins, where the differences
99