Strategies and methods in monitoring and targeting protein-protein interactions.

Protein-protein interactions are intrinsic to virtually every cellular process ranging from cell cycle control, DNA replication, transcription, splicing and translation, to intermediary metabolism, secretion, formation of cellular macrostructures and enzymatic complexes. Apart from a variety of stable protein-protein interactions, there are a plethora of transient protein-protein interactions that control and regulate a large number of cellular processes. All modifications of proteins involve such transient protein-protein interactions. Indeed, glycosyl transferases, acyl transferases, kinases, phosphatases, and proteases interact only transiently with their protein substrates. Such protein-modifying enzymes encompass a large number of fundamental processes such as signal transduction, cell growth, and metabolic pathways. Since protein-protein interactions play a role in nearly all events that take place in a cell, information on the function of an unknown protein can be obtained by investigating its interaction with other proteins whose functions are already known. Thus, if the function of one protein is known, then the function of its binding partner is likely to be related. This concept has been called “guilt by association” and allows the researcher to employ a relatively small number of functionally characterized proteins and to quickly assign functions to their uncharacterized binding partners. Moreover, alteration of protein-protein interactions is known to contribute to many diseases. As an example, tumor-forming viruses cause uncontrolled proliferation of the host cell by dissociating important protein-protein interactions between regulatory proteins of the cell cycle. Hence, the manipulation of protein-protein interactions that contribute to disease is a potential therapeutic strategy. The contact surfaces of the protein complexes have unique structure and properties and they are more conservative in comparison with active site of enzymes. So they represent prospective targets for a new generation of drugs. During the last decade, numerous investigations were undertaken to find or design small molecules that block protein dimerization or heterologous protein-protein interactions [2]. To date, a variety of genetic and biochemical methods exist for studying protein-protein interactions and identifying inhibitors of such interactions. This chapter describes recent developments in proteomic research. In more detail, the first part of this chapter focuses on technologies recently developed in protein interaction investigation, i.e. yeast two-hybrid screens, phage display, protein microarray technology, two-dimensional electrophoresis coupled to mass spectroscopy, etc. Different strategies are compared; problems that are encountered in studying protein-protein interactions, solutions to these problems, advantages and limitations of various methods and techniques are also discussed. The second part presents recent approaches to identify and characterize new inhibitory molecules that act by disrupting biologically relevant protein-protein interactions. In particular, screening strategies that employ variants of the technologies reviewed in the first part of this chapter are discussed.