Modelling and systems approaches for elucidating information processing in multi-site phosphorylation systems
Creators: name: Suwanmajo, Thapanar
Publisher: name: Imperial College London
Year: 2016

description: Multisite phosphorylation is a basic ingredient of cellular signalling and information processing and involves the modification of substrates by kinases and phosphatases at multiple locations. Multisite phosphorylation (and modification in general) has emerged as a key underlying mechanism by which cells exhibit control different aspects of their functioning and decision making. In the past decade, various studies have focussed on the behaviour of multisite phosphorylation, theoretically, analysing both distributive and processive mechanisms of multisite phosphorylation. There have also been a number of experimental studies in multisite phosphorylation in a range of cellular pathways and contexts. While these studies have provided important insights, there is a significant gap in understanding the role of multisite phosphorylation and its role in signalling pathways. In this thesis, a structured modelling and systems engineering approach is employed to elucidate different aspects of multisite phosphorylation and its role in cellular pathways. This is developed through a series of investigations. The first investigation demonstrates that distributive multisite phosphorylation systems can exhibit a biphasic dose response thus demonstrating an in-built competing effect in the modification mechanism, a feature not shared by processive mechanisms. A series of analyses is able to pin down when this biphasic response will and will not occur. In the second investigation, the main focus is on the effect of the modification mechanism on information processing characteristics. A framework is developed to analyse the interplay between distributive and processive mechanisms leading to mixed mechanisms. Analysis of mixed mechanisms shows that bistablility and biphasic dose response curves can be eliminated as a consequence of the interplay of distributive and processive mechanisms. On the other hand, the interplay between these two mechanisms can result in sustained oscillations. In the third investigation, a structured systems framework is developed to bridge the gap between the multisite phosphorylation module in isolation and as part of networks and pathways. To this end, a comprehensive in silico analysis is performed to examine the effect of enzyme activation, the effect of retroactivity associated with an output of the multisite module participating in downstream pathways, the effect of substrate (or enzyme) production and degradation, and also the effect of embedding the multisite module in different network modules. These studies provide a whole range of insights into qualitative transitions in behaviour associated with the effect of ambient network on the multisite module. The final investigation focuses on examining the effect of multiple kinases and/or phosphatases in multisite phosphorylation. Through an examination of ordered and random mechanisms this study demonstrates how the presence of a common substrate can couple different pathways. This study also demonstrates what kinds of information processing capabilities and constraints arise with multiple kinases. Taken together, a series of investigations provide a consolidated systems view of different aspects of multisite phosphorylation and as part of networks. This provides a consolidated platform and framework from which to investigate the effect of multisite phosphorylation in a range of specific natural contexts and to rationally engineer different aspects of biochemical pathways containing multisite phosphorylation.