Thesis final - after defense-7 - Jacobs University

Chapter 3
3.1.2.3. Towards an in silico approach for the downstream processing of bioproducts
The in silico approach is actually the computational models or simulations based on the
experimental data which can be used for making hypothesis and predictions about any
biological process (83, 84). This approach has been widely used in the pharmaceutical
industry for drugs discovery as discussed in chapter 1. However, the in silico approach was
rarely evaluated in practical terms for the downstream processing of proteins. Several research
groups had proposed models for the prediction of the chromatographic behavior of proteins
onto hydrophobic adsorbents with varying degrees of success but none of these approaches
have gained a universal acceptance (26, 87, 103). The first and major criticism was that all the
schemes were based on model proteins instead of real biological crude extract. The second
criticism was that how can one predict about the separation of any specific protein from
biological mixtures based on the data of few homologous model proteins and without
considering the chromatographic fractionation of the host cell proteome. The third criticism
was that those models were based on the retention time and / or volume of the model proteins
and these two parameters have no applicability in terms of real bioprocess. At any specific
space of time (minute), several proteins are supposed to be eluted instead of a single protein
during chromatographic fractionation of a cell proteome. Instead of retention time and / or
volume, the salt concentration should be specified for the protein elution under specific
chromatographic conditions. They never tried a model based on the chromatographic
separation of the total cell proteome as the approach is experimentally demanding and
laborious. This approach has been adopted in this work as presented in Figure 10, where
several techniques were employed ranging from chromatographic fractionation of cell
proteome to identification and analysis of the proteins available in each chromatographic
fraction. The identified proteins were characterized by several protein properties and these
properties were then further correlated to the chromatographic behavior. The protein
properties were also investigated for their ability to differentiate among the adsorbents. Aside
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