Computational interaction proteomics: from proteome to complexome

Abstract

Modern measurement methods and computational data analysis tools allow protein exploration that covers all proteins in an organism. Especially discovering the interactions between the proteins is crucial for a better understanding of the cell, because proteins in the cell do not carry out their function alone but in close cooperation with other proteins. Protein interaction takes place at different levels. At a low level, proteins are bound firmly, building stable and small complexes. At a higher level, the small stable complexes themselves interact with other complexes to build larger assemblies, and one such complex is often part of many different assemblies. Considering the different levels of protein interactions has caused a shift of thinking in modern interaction proteomics. The focus changed from treating interactions equally to a subtle distinction between binary interactions, stable small complexes and larger assemblies up to the interaction between protein complexes. This paradigm change is called the transition from proteomics to complexomics and strives for observing a broader picture of protein interactions. This thesis follows that novel way of thinking and combines my complexome research of the last four years. It contains an overview of IP/MS based interaction proteomics and presents several novel methods to detect protein interaction at the different interaction levels